JP2016509228A - Method - Google Patents

Abstract

The present invention is a method for assisting in the detection of surface abnormalities of a subject's esophagus, wherein the surface abnormalities are mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and mucosa. Selected from the group consisting of internal cancer (IMC), wherein the method comprises: a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus And b) said cells are selected from (i) p53; (ii) c-Myc; (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3. Assaying for a marker, wherein detection of at least two abnormal levels of the marker means that the likelihood of a surface abnormality of the subject's esophagus is increased Regarding the law. The invention also relates to certain kits, devices and uses.

Description

  The present invention is in the field of examining or assisting in the detection of esophageal surface abnormalities.

  Esophageal cancer (OAC, oesophageal cancer) is the eighth most common type of cancer in the world, and its incidence has increased almost five-fold over the past 30 years.

  Barrett's esophagus is the first step in the path to OAC, and meta-analysis demonstrates that Barrett's esophagus results in an increased risk of progression to adenocarcinoma of 0.12-0.5% per year Yes. Barrett's esophagus occurs when normal esophageal cells are replaced by glandular cells and progresses over time to mild dysplasia (LGD), high-grade dysplasia (HGD), and finally to adenocarcinoma. Can do.

  Early diagnosis of OAC and / or its precancerous precursor Barrett's esophagus can improve patient management and prognosis of OAC. In one known approach, a Cytosponge ™ cell collection device has been developed, for example as published in WO 2011/058316.

  In addition, tests using TFF3 as a molecular marker have been developed by Fitzgerald et al as a clinical screening tool to detect Barrett's esophagus, for example as published in US Patent Application Publication No. 201201009597. .

  First study using Cytosponge ™ (BEST1) (Kadri, SR, Lao-Sirieix, P., O'Donovan, M., Debiram, I., Das, M., Blazeby, JM, Emery, J. , Boussioutas, A., Morris, H., Walter, FM, et al. (2010) .Acceptability and accuracy of a non-endoscopic screening test for Barrett's oesophagus in primary care: cohort study.BMJ 341, c4372) The TM test proved to be a suitable method for diagnosing Barrett's esophagus in a primary care environment.

  In current systems, symptomatic patients are sent to endoscopy. Endoscopy is an invasive procedure that requires a highly trained clinician. Endoscopy is an uncomfortable procedure for the patient and may require sedation. If a biopsy is involved with endoscopy, patients undergoing this procedure are also at some risk. In the clinical environment, this is currently the only method of detecting Barrett's esophagus and / or dysplasia or cancer with Barrett's esophagus.

  Rugge et al (Rugge, M., Fassan, M., Zaninotto, G., Pizzi, M., Giacomelli, L., Battaglia, G., Rizzetto, C., Parente, P., and Ancona, E. ( 2010). Aurora kinase A in Barrett's carcinogenesis. Hum Pathol 41, 1380-1386) discloses Aurora kinase A (AURKA) in Barrett's esophageal cancer development. It was pointed out that the TP53 mutation is recognized as a marker for increased risk of Barrett's esophageal adenocarcinoma. Esophageal biopsy samples were obtained from the long segment of Barrett's esophagus. Nine of 10 Barrett's esophageal adenocarcinomas showed AURKA immunostaining. AURKA expression was examined by mRNA analysis and microarray studies. The authors concluded by attributed a significant role in AURKA overexpression in the progression of Barrett mucosa to cancer. The authors concluded that in a larger and prospective study, further efforts were needed to validate AURKA IHC expression as a possible prognostic marker in patients with Barrett mucosa.

  Liu et al (2008 World Journal of Gastroenterology vol 14 pages 7199-7207) discloses a tissue array of Tp53, C-myc, CCND1 gene overexpression in different tumors. Seven different types of tumors were examined. The analysis was nucleic acid based. The sample used was from a known tumor. No detection method is taught. Samples were fixed with formalin.

  Agnese et al (2007 European Society for Medical Oncology vol 8 Suppl 6 vi110-vi115) discloses aurora A overexpression as an early marker of reflux-associated columnar mucosa and Barrett's esophagus. The authors reported that AURKA mRNA expression between Barrett's esophageal mucosa (columnar lined oesophagus) and Barrett's oesophagus (BO) with or without dysplasia and p53 positive immunostaining A small, statistically significant amount of difference could not be found.

  Several molecular markers have been studied in connection with Barrett's esophagus. These markers have been studied purely in the context of research. These studies have been performed on tissue samples in vitro. These markers have been studied alone. At present, there is no such molecular marker used in clinical trials for Barrett's esophageal-related abnormalities.

WO 2011/058316 pamphlet US Patent Application Publication No. 20120009597

Kadri, SR, Lao-Sirieix, P., O'Donovan, M., Debiram, I., Das, M., Blazeby, JM, Emery, J., Boussioutas, A., Morris, H., Walter, FM , et al. (2010). Acceptability and accuracy of a non-endoscopic screening test for Barrett's oesophagus in primary care: cohort study.BMJ 341, c4372 Rugge, M., Fassan, M., Zaninotto, G., Pizzi, M., Giacomelli, L., Battaglia, G., Rizzetto, C., Parente, P., and Ancona, E. (2010). Aurorakinase A in Barrett's carcinogenesis. Hum Pathol 41, 1380-1386 Liu et al (2008 World Journal of Gastroenterology vol 14 pages 7199-7207) Agnese et al (2007 European Society for Medical Oncology vol 8 Suppl 6 vi110-vi115)

  There is a need in the art for improved detection of Barrett's esophageal related abnormalities. Prior art tests are expensive, labor intensive, invasive, and involve risks to the subject being tested.

  The present invention seeks to overcome the problems associated with the prior art.

  Certain molecular markers have been shown to be associated with Barrett's esophageal related abnormalities. These markers have been studied by tissue biopsy. The use of molecular markers for tissue biopsy offers little practical advantage over biopsy morphological examinations, which are currently clinically representative. This is because studying markers in this manner still requires the biopsy to be collected, which still entails each of the problems associated with invasive procedures in the prior art. . More importantly, a single marker studied in the context of the study exhibits an inappropriate sensitivity and / or inappropriate specificity to be recognized as a robust marker that contributes to detection or diagnosis.

  The inventors have studied a wide range of candidate markers. We have also studied these markers in different combinations. We have reached a small, clear panel of markers that yields clinically useful sensitivity and specificity scores when tested in combination. In addition, we studied the performance of these markers in surface sampling cells. For example, the combination of these markers can be used to analyze cells recovered from esophageal surface sampling, such as obtained using a cell recovery device such as Cytosponge ™.

  The method we teach involves a novel combination of markers not previously used in clinical trials. In addition, we demonstrate that these markers can be used when used on cells obtained from esophageal surface sampling and produce reliable results. In addition, these various features of the method of the present invention provide the advantages of a robust and clinically useful risk assessment while advantageously avoiding the need for invasive tissue retrieval by biopsy. These and further advantages of the present invention are described in greater detail below.

Thus, in a broad aspect, the invention is a method for assisting in detecting surface abnormalities in a subject's esophagus,
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
(Iii) AURKA or PLK1, preferably AURKA;
(Iv) methylation of MyoD and Runx3; and (v) assaying for at least two markers selected from atypical,
Detection of at least two abnormal levels of the marker provides a method that means that there is an increased likelihood of a surface abnormality of the subject's esophagus.

In another aspect, the present invention is a method for assisting in detecting a surface abnormality of a subject's esophagus, wherein the surface abnormality is mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma. (OAC, oesophageal adenocarcinoma) and intramucosal cancer (IMC) selected from the group consisting of:
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3;
Detection of at least two abnormal levels of the marker relates to a method which means that the likelihood of a surface abnormality of the subject's esophagus is increased.

More suitably, in one aspect, the present invention is a method for assisting in detecting surface abnormalities in a subject's esophagus, comprising:
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
(Iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3;
Assaying for at least two markers selected from
Detection of at least two abnormal levels of the marker provides a method that means that there is an increased likelihood of a surface abnormality of the subject's esophagus.

The markers described herein are shown with guidance on absolute scoring for each marker. This has the advantage of introducing a reference standard / comparison step into the already analyzed scoring system. However, if desired, the present invention can alternatively function by comparison with a reference standard, eg, from a healthy (no esophageal abnormality) subject. Thus, in one aspect, the present invention is a method for assisting in detecting surface abnormalities of a subject's esophagus,
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3;
Detection of at least two abnormal levels of the marker as compared to a reference standard provides a method that means that the likelihood of a surface abnormality in the subject's esophagus is increased.

Step (b)
(1) The cells are
(I) p53;
(Ii) c-Myc;
Contacting (iii) AURKA; and (iv) a reagent for detecting at least a first molecular marker selected from methylation of MyoD and Runx3;
(2) detecting at least a second molecular marker selected from (i) to (iv) and / or contacting said cell with a reagent for assaying said cell for atypical You may go out.

More suitably, step (b) comprises
(1) The cells are
(I) p53;
(Ii) c-Myc;
Contacting (iii) AURKA; and (iv) a reagent for detecting at least a first molecular marker selected from methylation of MyoD and Runx3;
(2) contacting the cell with a reagent for detecting at least a second molecular marker selected from (i) to (iv).

  The surface abnormality may be selected from the group consisting of mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and intramucosal cancer (IMC). These all share the property of being “glandular” (“columnar”). All of these share characteristics that are of the “Barrett's esophagus”. All of these are dysplasias. None of these are squamous epithelia.

  Suitably the present invention is not related to squamous dysplasia.

  Suitably the present invention does not relate to squamous cell carcinoma.

  Suitably, the surface abnormality is not related to the squamous cell abnormality.

  The surface abnormality may be selected from the group consisting of mild dysplasia (LGD), severe dysplasia (HGD), and intramucosal cancer (IMC).

  The surface abnormality may be selected from the group consisting of mild dysplasia (LGD) and severe dysplasia (HGD).

  The surface abnormality may be selected from the group consisting of asymptomatic esophageal adenocarcinoma (OAC) and intramucosal cancer (IMC).

  The surface abnormality may be mild dysplasia (LGD).

  The surface abnormality may be high dysplasia (HGD).

  The surface abnormality may be asymptomatic esophageal adenocarcinoma (OAC).

  The surface abnormality may be intramucosal cancer (IMC).

  Abnormal levels of at least three of the markers may be assayed.

  Abnormal levels of at least four of the markers may be assayed.

  The abnormal level of each of the markers may be assayed.

  The cells may be recovered by unbiased sampling of the surface of the esophagus.

  The cells may be collected using a capsule sponge.

  Before contacting the cell with a reagent for detecting the molecular marker, the cell is (i) pelleted by centrifugation, (ii) resuspending the cell in plasma, and (iii) thrombin. In addition, it may be prepared by incubating until a clot is formed. Preparation may further include incubating the clot in formalin, processing to paraffin blocks, and slicing into appropriate sections for microscopy.

  p53 may be evaluated by immunohistochemistry.

  p53 may be evaluated at the nucleic acid level. The p53 mutation state may be evaluated (for example, detected). p53 mutations may have been evaluated (eg, detected) by sequencing. Suitably, when p53 is detected at the nucleic acid level, “abnormal level detection” means detection of a p53 mutation. In other words, the detection of a p53 mutation is itself considered an abnormal p53 or an abnormal level of p53. Assessing p53 at the nucleic acid level has the advantage of removing or improving the subjectivity that may exist when assessing the staining level, eg, at the protein level for p53.

  Suitably, a p53 mutation anywhere in the p53 gene is detected. This is advantageous because the mutation can spread through the gene. More suitably, mutations in the DNA binding domain are detected. These are the most common mutations. Suitably the assay can detect mutations through the gene. If further guidance is required, see Example 10 for further details.

  Suitably, a p53 mutation is detected when a p53 nonsense mutation is detected. Suitably, a p53 mutation is detected when a p53 missense mutation is detected. Suitably, a p53 mutation is detected when a p53 deletion mutation is detected. Suitably, a p53 mutation is detected when a p53 indel variant mutation is detected.

  Suitably the p53 mutation is one mentioned in Example 10.

  Suitably the p53 mutation is one in the DNA binding domain of p53.

  p53 may be evaluated at both nucleic acid and protein levels. This captures any mutations that are not detected by the protein assay (eg, p53 mutations that do not affect p53 expression / detection) and any non-p53 changes that affect p53 expression (eg, mutations in genes other than p53). Provide the advantage of being (ie, by protein analysis).

  Suitably p53 is assessed by detection of one or more p53 mutations.

  Suitably p53 is assessed by immunohistochemistry and p53 is also assessed by detection of one or more p53 mutations.

  cMyc may have been evaluated by immunohistochemistry.

  AURKA may have been evaluated by immunohistochemistry.

  It should be noted that AURKA is a preferred marker of the present invention. However, it is recognized that the marker PLK1 also has good sensitivity (91%) and good specificity (88%). This biomarker was excluded in favor of AURKA as AURKA showed better sensitivity (93%) and specificity (94%) data (see Examples). However, we teach that overexpression of AURKA or PLK1 detects essentially the same case. Thus, in an embodiment of the invention, PLK1 may be assayed instead of (or in addition to) AURKA. Thus, suitably AURKA or PLK1, preferably AURKA is assayed.

  MyoD / Runx3 methylation may be assayed by MethyLight analysis.

  Atypical may be assessed by scoring cells for their morphology according to the Wien scale. Suitably, the Vienna scale is as described in Schlemper et al 2007 Gut 2000; 47: 251-255.

  In another aspect, the invention relates to a method as described above, wherein the step of assaying said cells for TFF3 precedes step (b) of said method.

In another aspect, the invention provides an assay for selecting a treatment regimen comprising:
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3;
It relates to an assay for selecting a treatment regimen for endoscopy and biopsy if at least two abnormal levels of said marker are detected.

In another aspect, the invention provides:
(A) configured to analyze an esophageal sample from a subject, said analysis comprising:
(B) the cells
(I) p53;
(Ii) c-Myc;
A device or system comprising the step of assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3,
Including output module,
If at least two abnormal levels of the marker are detected, the output module relates to an apparatus or system that indicates an increased likelihood of surface abnormalities in the esophagus for the subject.

  In another aspect, the invention relates to a substance that recognizes, binds to, or has affinity for the methylation of a polypeptide or a nucleic acid sequence for use in assisting in the detection of surface abnormalities in the subject's esophagus Wherein the polypeptide and / or nucleic acid sequence is, for example, methylation of p53, c-Myc, AURKA, Runx3 / MyoD1, as defined above. In another aspect, the invention relates to such use of a combination of substances each recognizing, binding to or having affinity for one or more of said polypeptide or nucleic acid sequences, respectively.

  In another aspect, the present invention is an assay device for use in assisting in the detection of surface abnormalities in a subject's esophagus, which recognizes, binds to or has an affinity for methylation of a polypeptide or nucleic acid sequence. An assay device comprising a solid substrate having a location containing a substance having a property, wherein the polypeptide and / or nucleic acid sequence is, for example, p53, c-Myc, AURKA, Runx3 / MyoD1 methylation as defined above About.

In another aspect, the invention provides (i) p53 in a biological sample;
(Ii) c-Myc;
(Iii) AURKA
And a reagent for determining the methylation level of MyoD and Runx3.

  In another aspect, the invention provides a method for assisting in detecting a surface abnormality of a subject's esophagus, the method comprising providing a sample of cells from the subject, wherein the sample is from the surface of the subject's esophagus. Including recovering cells; and assaying said cells for TFF3, wherein if TFF3 is detected in the cells of the sample, performing the above method, and in addition to detecting TFF3, at least 1 The detection of an abnormal level of one marker relates to a method indicating that the likelihood of a surface abnormality of the subject's esophagus is increasing.

In another aspect, the present invention is a method for assisting in detecting a surface abnormality of a subject's esophagus, comprising:
(A) providing a sample of cells from the subject and assaying the cells for TFF3, the sample comprising cells recovered from the surface of the subject's esophagus, wherein TFF3 is detected in the sample cells If so, perform the following additional steps:
(B) the cells
(I) p53;
(Ii) c-Myc;
(Iii) AURKA; and (iv) assaying for at least two markers selected from methylation of MyoD and Runx3, wherein detection of an abnormal level of at least one marker in addition to detection of TFF3 comprises said subject It relates to a method of indicating that the possibility of surface abnormalities of the esophagus is increasing. At least two markers in addition to detection of TFF3, preferably at least three markers in addition to detection of TFF3, preferably at least four markers in addition to detection of TFF3, preferably abnormalities of each of the markers in addition to detection of TFF3 Level detection may indicate an increased likelihood of a surface abnormality of the subject's esophagus. The cells may be recovered by unbiased sampling of the surface of the esophagus. The cells may be collected using a capsule sponge.

  In another aspect, the invention relates to a method of collecting information useful for detecting esophageal abnormalities comprising performing the above steps.

  In another aspect, the present invention relates to a method of collecting information useful for assisting diagnosis of esophageal abnormalities, comprising performing the above steps.

  In another aspect, the present invention relates to a method for diagnosing esophageal abnormalities comprising performing the above steps.

  In another aspect, the present invention relates to a method for assisting diagnosis of esophageal abnormalities, comprising performing the above steps.

  In another aspect, the invention relates to a method for assessing the risk of multiple esophageal abnormalities comprising performing the above steps.

  In another aspect, the invention relates to a method for assessing the risk of one esophageal abnormality comprising performing the above steps.

  The abnormality may be dysplasia. The abnormality may be LGD, HGD, IMC or asymptomatic OAC.

  In another aspect, the present invention provides a method for assisting in detecting a surface abnormality of an esophagus of a subject, wherein the surface abnormality is esophageal adenocarcinoma (OAC), and the method uses a sample of cells from the subject. Providing, wherein the sample comprises cells recovered from the surface of the subject's esophagus, and assaying the cells for SMAD4, where SMAD4 is detected in the cells of the sample, It relates to a method that is shown to increase the likelihood of esophageal adenocarcinoma (OAC) of the subject's esophagus.

  The present invention is particularly applied to the assessment of the risk of subjects with dysplasia. Currently, assessment of dysplasia is only performed on biopsies collected from subjects. In accordance with the present invention, a subject can be assessed for risk of having dysplasia (eg, one or more of LGD, HGD, IMC, which may include asymptomatic OAC) by the methods described herein. These methods advantageously avoid biopsy. The method of the present invention properly and explicitly eliminates biopsies. The method of the present invention advantageously requires only esophageal surface sampling (or in vitro samples from the surface of the esophagus), thus avoiding biopsy and / or endoscopy.

  Thus, an important part of the present invention is to use a panel of markers to assess the risk of a subject having dysplasia such as one or more of LGD, HGD or IMC.

  OAC is more typically considered to be an invasive type of disease, typically patients with OAC already exhibit symptoms, and typically the methods of the invention represent (for example) a diagnosis of OAC Rather, it is used for screening or surveillance applications and risk assessment applications. Infiltrating OAC is typically diagnosed using different algorithms that are not part of the present invention. However, asymptomatic OAC (or more precisely, increased risk of asymptomatic OAC) is in the same manner as LGD / HGD / IMC (or more precisely, increased risk of LGD / HGD / IMC). It can be detected by the method of the present invention. This has been done by the inventors. The invention was used in the manner described herein. Results using such a method indicated a higher risk of abnormality / dysplasia in the subject. Subjects were encouraged to undergo endoscopy / biopsy as a result of finding higher risk in accordance with the present invention. Endoscopy / biopsy revealed asymptomatic OAC. The patient was then referred to the appropriate treatment. Thus, although the present invention can be used to assess the risk of abnormalities / dysplasias that can include asymptomatic OAC, the present invention is not meant to be a diagnostic tool that provides a definitive diagnosis of OAC.

Subject / Patient Group Suitably, the method of the invention is used on any subject. Suitably, the method of the invention is used for any subject suspected of having Barrett's esophagus. These uses can be useful for screening the entire population.

  More suitably, the methods / panels of the present invention are applied to subjects or patients who are not known to have carcinoma but may be monitored or followed up for Barrett's esophagus.

  More suitably, the method of the present invention is used for any subject having Barrett's esophagus.

  The present invention assists in assessing the risk of progression in subjects who already have Barrett's esophagus or the risk of having LGD / HGD / IMC, which is an important advantage of the present invention.

  The panel of the present invention is not intended to detect Barrett's esophagus but is intended to assess the risk of having dysplasia. Assessment of having Barrett's esophagus is typically done using the established TFF3 marker of Barrett's esophagus or may be done by any suitable method for diagnosis of Barrett's esophagus.

  An important marker of Barrett's esophagus is the TFF3 marker. (Ie TFF3 positive in cells sampled from the surface from capsule sponges such as eg Cytosponge ™. Such subjects have no dysplasia, mild dysplasia, high dysplasia or dysplasia It is also conceivable that the patient may have undiagnosed superficial intramucosal carcinoma, but the main advantage of the present invention is that it is from the starting point that already has Barrett's esophagus. Of course, in assessing the risk of having dysplasia, the panel / method of the present invention can be used as a general screening tool for asymptomatic subjects, which is not considered economical. (Although this is of course very effective.) Therefore, for economic and practical reasons, the present invention is an object already at risk of dysplasia, It is optimally applied to screening patients who already have Barrett's esophagus.

  Suitably the subject has Barrett's esophagus.

  Suitably, the subject is positive for testing surface-sampled esophageal cells for TFF3.

  In one embodiment, the test for TFF3 may precede the test (panel) of the present invention. This serves as a useful internal control. If the subject was known to have Barrett's esophagus, the surface sampled cells should be positive for TFF3. Thus, if the subject's esophageal surface sample known to have Barrett's esophagus is negatively tested for TFF3, this may indicate that the sample is inadequate (eg, insufficient cells, or lack of columnar cells, or Some other problem). Resample from the surface of the subject's esophagus, retest for TFF3, and use the panel of the present invention only if a positive result is observed for TFF3 showing a reliable / solid sample from a patient with Barrett's esophagus It is recommended to proceed to the test.

  The inventors, among other things, designed BEST2, a multicenter prospective case-control study, with the goal of recruiting 1,000 patients, and this study was compared to endoscopic examination in Barrett's esophagus. This was done to test the performance characteristics of Cytosponge ™ to diagnose In addition, within BEST2, a panel of risk stratified biomarkers is evaluated with Cytosponge ™ to determine their ability to stratify patient risk according to the degree of dysplastic endoscopy. The panel of risk stratified biomarkers consists of four different biomarkers: p53 protein level, c-MYC protein level, Aurora kinase A (AURKA) protein level and Runt-related transcription factor 3 (RUNX3) and myogenic differentiation 1 ( MYOD1) consisting of methylation of the promoter region of the gene. The panel may further include atypicality that is a fifth marker.

Sample and Sample Recovery Suitably, the sample comprises cells from the subject of interest. Suitably the sample comprises esophageal cells from the subject of interest. Suitably the sample is not obtained by endoscopy, i.e. the sample is suitably obtained without using an endoscope.

  Sampling by endoscopy is an invasive technique. Furthermore, endoscopic sampling is a targeting technique in which biopsies are taken at intervals along the esophagus, or an operator visually identifies damage, particularly targeted for biopsy.

  Suitably, the present invention does not include an endoscopic sample such as an endoscopic biopsy.

  An important principle of the present invention is to provide a test specific to esophageal abnormalities. The test is specific in the sense that it does not result in problematic false positive levels from cells of unrelated tissue such as normal squamous esophagus or gastric cardia (stomach). Thus, by providing a test having these specific characteristics, the present invention advantageously provides a test aimed at detecting abnormal esophageal cells. In this way, the present invention advantageously avoids the need for targeted sample collection. Thus, the present invention advantageously includes samples obtained by non-targeted sample collection such as sampling the entire surface of the esophagus rather than targeting only the area of suspicious damage (Barrett's esophagus).

  Thus, suitably the sample does not include a biopsy by endoscopy.

  Suitably the sample may comprise esophageal brushing or surface cells. Esophageal brushing can be obtained using an endoscope or other means. Suitably, if the sample includes esophageal brushing, the esophageal brushing is obtained by means not by endoscopy.

  Suitably, the sample comprises cells from the surface of the subject's upper intestinal tract.

  Suitably the sample consists of cells from the surface of the upper intestinal tract of the subject.

  Suitably, the sample may comprise cells sampled from the entire esophageal lumen.

  Suitably, the sample may contain both esophageal cells and non-esophageal cells.

  Suitably the sample may comprise esophageal cells together with gastric cardia cells.

  Suitably the sample may consist of esophageal cells.

  Suitably, the sample comprises cells from the surface of the subject's esophagus.

  Suitably, the sample consists of cells from the surface of the subject's esophagus.

  Most suitably, the sample may contain cells collected using a capsule sponge type sampling technique.

  Particularly suitable sampling techniques are described in the Examples section.

  Examples of suitable samples include esophageal brushing (either obtained by endoscopy or not by endoscopy), samples obtained by balloon cytology, samples obtained by capsule sponge sampling. Including. Most suitably, the sample comprises cells obtained by capsule sponge sampling.

  The panel of markers relates to luminal surface cells. This means that the sample to be analyzed need only be recovered from the surface of the esophageal lumen. This advantageously avoids the need for biopsy, such as endoscopic biopsy. In addition, this advantageously avoids the need to preserve tissue structure in the sample to be analyzed.

  A further advantage of the markers of the present invention is that these markers are selected to avoid false positives caused by cells recovered from the gastric mucosa (eg gastric cardia / stomach). This has the particular advantage that if the sample contains gastric mucosal cells, the panel can still function as an esophageal abnormality detection mode. This is because the marker is not found in gastric mucosal cells, and therefore false positives do not occur even if the sample contains gastric mucosal cells.

  Thus, it can be appreciated that the selection of markers in the panel by the inventors results in a degree of specificity not yet provided by any prior art approach to screening for esophageal abnormalities. The inventors have succeeded in initially actively seeking and bringing about such a focused discriminating panel.

  Non-endoscopic capsule sponge devices used in previous clinical studies (eg UK reference number: CI / 2007/0053) may be used for sample collection. Preliminary studies have demonstrated that this device (“Cytosponge ™”) is acceptable to patients and can be used in primary care. The device consists of a polyurethane sponge tied to a string and encapsulated in a gelatin capsule. The capsule is swallowed and dissolves in the stomach after 3-5 minutes.

  Suitably, the collected cytology specimen is processed into a pellet, which is then embedded in paraffin, thereby preserving the tissue structure. This can then be subjected to a histological assessment, and more than one molecule and / or morphological marker may be used for a single sample. Thus, this aspect of sample collection is particularly suitable for use in the present invention.

  Cells are appropriately sampled from the surface of the esophagus using a swallowable abrasive material, which is collected from the patient and then separated for analysis to determine the presence of the marker. .

  Preferably, substantially the entire surface of the esophagus, preferably the entire surface, is sampled.

  Abrasive means that the material can remove cells from the inner surface of the esophagus. Obviously, this means to be used in the subject's esophagus, so “abrasiveness” must be interpreted in view of the application. In the context of the present invention, the term “abrasive” has the meaning given above, which means that the material is passed through the esophagus in an appropriate amount / configuration and to determine if cells have been removed from the esophagus. Can be tested by examining

  The material used in the collection device must be sufficiently abrasive to sample any dysplastic cells present in the esophagus. Preferably, the material is sufficiently abrasive to sample any Barrett's esophagus or dysplastic or adenocarcinoma cells present. In the most preferred embodiment, preferably the material is sufficiently abrasive so that the entire esophagus can be sampled, i.e., any Barrett's esophagus and / or circles where some squamous cells may be present. Collected along with columnar and / or adenocarcinoma cells. This is because bullets are easier to remove than normal squamous cells if their sampling is removed by the material, as squamous cells are more difficult to remove than dysplastic cells. The possibility of not sampling the cells of interest, such as esophagus or dysplastic cells (if present), is therefore advantageous as it provides the operator with a small control.

  Preferably, the swallowable abrasive material is inflatable. In this embodiment, preferably the abrasive material is smaller in size when swallowed than when removed. The expandable material may simply be a resilient material that has been compressed to expand back to a substantially uncompressed size when released from compression. Alternatively, this may be a material that expands, for example, by sucking up an aqueous fluid to a final size that exceeds its original size.

  In other words, preferably the device material expands, swells, increases or increases in size between swallowing and removal. Preferably, the device is self-expandable, i.e. does not require further intervention between swallowing and expansion. Preferably the device is not extendable. Preferably, after removing the restraint after swallowing, the device expands by unfolding, spreading, unrolling, or growing in size. Preferably, the device material is compressible and returns to an approximately uncompressed size after swallowing. Preferably, the device is comprised of a compressed material that is constrained in a compressed state so as to be releasable. Preferably, the material is released from restraint after swallowing to allow the device / material to expand prior to removal.

  Preferably, the device comprises a compressible material compressed in the form of a capsule. Preferably, the compressible material is in the form of a sponge material. Preferably, the compressed sponge is at least partially surrounded by a soluble and / or digestible coating, such as a capsule coating. Preferably the sponge is indigestible. Preferably, the capsule coating is formed at least partially from gelatin. Preferably, the capsule coating is formed entirely of gelatin.

  In one embodiment, it may be desirable to make the entire device out of digestible material to increase safety if the device is lost in the subject. Of course, the abrasive material needs to be digested at a slower rate than the capsule, and the string would need to be digested as well. Preferably, the abrasive material is non-digestible. Preferably the string is non-digestible.

  Preferably, the abrasive material comprises polyurethane, preferably polyurethane sponge.

  Suitably, the abrasive material is compressible. Suitably, the abrasive material comprises a reticulated polyurethane.

  Suitably the material has a uniform shape.

  Suitably the material has a uniform diameter.

  Suitably, the uncompressed shape is circular, such as spherical.

  Suitably, the uncompressed diameter is 3 cm.

  Suitably, the strap is connected to the abrasive material by a loop of cords disposed below the surface of the abrasive material, the ring being closed by a hook knot.

  Suitably, the abrasive material is compressed, wherein the abrasive material remains compressed by a soluble capsule.

  Suitably, the soluble capsule comprises a gelatin capsule.

  Suitably, the capsule can be dissolved and the compressible and abrasive material can return to its uncompressed size within 5 minutes when immersed in water at 30 degrees Celsius.

  Preferably the device is a capsule sponge. As is apparent from the specification, a capsule sponge is a device that includes a compressible sponge as an abrasive material, wherein the sponge is compressed into a capsule shape, and the capsule-shaped compressed sponge is preferably made of gelatin. A device that is reversibly constrained to a compressed state by at least a partial coating of such soluble and / or digestible material. Preferably, the device is a capsule sponge as described in WO 2011/058316.

  Preferably, the sample does not contain material collected by endoscopy. Preferably, the sample does not include a biopsy by endoscopy. Preferably, the sample does not include brushing by endoscopy.

  Sampling is not directed to any particular part of the esophagus, e.g. visually directed, rather the sponge is scraped along the entire surface of the esophagus to obtain a heterogeneous sample of cells from the tube, This is a feature of the present invention. It is the present invention that a greater percentage of the esophageal surface is sampled than is achieved by prior art techniques such as endoscopic biopsy (sampling approximately 1% of the surface) or endoscopic brushing. Is a further advantage.

  Preferably at least 10% of the esophageal surface, preferably at least 20%, preferably at least 30%, preferably at least 40%, preferably at least 50%, preferably at least 60%, preferably at least 70%, preferably at least 80%. %, Preferably at least 90% is sampled. In the most preferred embodiment, preferably substantially the entire esophagus is sampled, preferably the entire inner lumen of the esophagus is sampled. This is equally true, for example, for in vitro samples where the method of the invention does not involve sample recovery.

  Suitably the sample is an in vitro sample.

  Suitably the sample is an in vitro sample.

Suitably, sampling of the cell surface of the upper intestinal tract, such as the esophagus,
(I) introducing into the subject a swallowable device comprising an abrasive material capable of recovering cells from the surface of the esophagus;
(Ii) retrieving the device by removing it through the esophagus;
(Iii) recovering cells from the device.

  Preferably, step (i) comprises introducing a swallowable device comprising an abrasive material capable of recovering cells from the surface of the esophagus into the subject's stomach.

  Suitably, the sample is from a white human subject.

  Suitably the sample is from a subject with a history of backflow.

  Suitably the sample is from a male subject.

  Suitably the sample is from an obese subject.

Methods of the Invention In one embodiment, suitably the method is an in vitro method. In one embodiment, suitably the method is an extracorporeal method. In one embodiment, suitably the actual sampling of cells is not part of the method of the invention. Suitably, the method does not include cell recovery.

  Suitably the sample is a previously collected sample. Suitably the method does not require the presence of the subject to which the cells are assayed. Suitably the sample is an in vitro sample. Suitably, the method does not include actual medical judgment in a narrow sense. Such determination in a narrow sense is typically performed by a doctor.

  Suitably the method of the invention is performed in vitro. Suitably the method of the invention is performed outside the body.

Markers used in the present invention

  The Genbank accession number is indicated with reference to the database as of the filing date of this application, that is, as of February 21, 2013. Where any further assistance is required, preferably the accession number shown here should refer to Genbank publication number 194.0, February 15, 2013.

  For purposes of illustration, an exemplary p53 sequence is shown below as obtained from GenBank.

Homo sapiens tumor protein p53 (TP53), transcription variant 1, mRNA
NCBI reference sequence: NM_000546.5
Accession Number NM_000546
Version NM_000546.5
origin
1 gatgggattg gggttttccc ctcccatgtg ctcaagactg gcgctaaaag ttttgagctt
61 ctcaaaagtc tagagccacc gtccagggag caggtagctg ctgggctccg gggacacttt
121 gcgttcgggc tgggagcgtg ctttccacga cggtgacacg cttccctgga ttggcagcca
181 gactgccttc cgggtcactg ccatggagga gccgcagtca gatcctagcg tcgagccccc
241 tctgagtcag gaaacatttt cagacctatg gaaactactt cctgaaaaca acgttctgtc
301 ccccttgccg tcccaagcaa tggatgattt gatgctgtcc ccggacgata ttgaacaatg
361 gttcactgaa gacccaggtc cagatgaagc tcccagaatg ccagaggctg ctccccccgt
421 ggcccctgca ccagcagctc ctacaccggc ggcccctgca ccagccccct cctggcccct
481 gtcatcttct gtcccttccc agaaaaccta ccagggcagc tacggtttcc gtctgggctt
541 cttgcattct gggacagcca agtctgtgac ttgcacgtac tcccctgccc tcaacaagat
601 gttttgccaa ctggccaaga cctgccctgt gcagctgtgg gttgattcca cacccccgcc
661 cggcacccgc gtccgcgcca tggccatcta caagcagtca cagcacatga cggaggttgt
721 gaggcgctgc ccccaccatg agcgctgctc agatagcgat ggtctggccc ctcctcagca
781 tcttatccga gtggaaggaa atttgcgtgt ggagtatttg gatgacagaa acacttttcg
841 acatagtgtg gtggtgccct atgagccgcc tgaggttggc tctgactgta ccaccatcca
901 ctacaactac atgtgtaaca gttcctgcat gggcggcatg aaccggaggc ccatcctcac
961 catcatcaca ctggaagact ccagtggtaa tctactggga cggaacagct ttgaggtgcg
1021 tgtttgtgcc tgtcctggga gagaccggcg cacagaggaa gagaatctcc gcaagaaagg
1081 ggagcctcac cacgagctgc ccccagggag cactaagcga gcactgccca acaacaccag
1141 ctcctctccc cagccaaaga agaaaccact ggatggagaa tatttcaccc ttcagatccg
1201 tgggcgtgag cgcttcgaga tgttccgaga gctgaatgag gccttggaac tcaaggatgc
1261 ccaggctggg aaggagccag gggggagcag ggctcactcc agccacctga agtccaaaaa
1321 gggtcagtct acctcccgcc ataaaaaact catgttcaag acagaagggc ctgactcaga
1381 ctgacattct ccacttcttg ttccccactg acagcctccc acccccatct ctccctcccc
1441 tgccattttg ggttttgggt ctttgaaccc ttgcttgcaa taggtgtgcg tcagaagcac
1501 ccaggacttc catttgcttt gtcccggggc tccactgaac aagttggcct gcactggtgt
1561 tttgttgtgg ggaggaggat ggggagtagg acataccagc ttagatttta aggtttttac
1621 tgtgagggat gtttgggaga tgtaagaaat gttcttgcag ttaagggtta gtttacaatc
1681 agccacattc taggtagggg cccacttcac cgtactaacc agggaagctg tccctcactg
1741 ttgaattttc tctaacttca aggcccatat ctgtgaaatg ctggcatttg cacctacctc
1801 acagagtgca ttgtgagggt taatgaaata atgtacatct ggccttgaaa ccacctttta
1861 ttacatgggg tctagaactt gacccccttg agggtgcttg ttccctctcc ctgttggtcg
1921 gtgggttggt agtttctaca gttgggcagc tggttaggta gagggagttg tcaagtctct
1981 gctggcccag ccaaaccctg tctgacaacc tcttggtgaa ccttagtacc taaaaggaaa
2041 tctcacccca tcccacaccc tggaggattt catctcttgt atatgatgat ctggatccac
2101 caagacttgt tttatgctca gggtcaattt cttttttctt tttttttttt ttttttcttt
2161 ttctttgaga ctgggtctcg ctttgttgcc caggctggag tggagtggcg tgatcttggc
2221 ttactgcagc ctttgcctcc ccggctcgag cagtcctgcc tcagcctccg gagtagctgg
2281 gaccacaggt tcatgccacc atggccagcc aacttttgca tgttttgtag agatggggtc
2341 tcacagtgtt gcccaggctg gtctcaaact cctgggctca ggcgatccac ctgtctcagc
2401 ctcccagagt gctgggatta caattgtgag ccaccacgtc cagctggaag ggtcaacatc
2461 ttttacattc tgcaagcaca tctgcatttt caccccaccc ttcccctcct tctccctttt
2521 tatatcccat ttttatatcg atctcttatt ttacaataaa actttgctgc cacctgtgtg
2581 tctgaggggt g

Atypical Atypical is evaluated by observation.

  Suitably, the cells are stained prior to observation. Suitably, the cells are stained using hematoxylin and eosin (H & E) staining. This has the advantage of easily distinguishing cells from each other according to conventional and long established histology.

  Identify cells using standard histology / cytology.

  Scoring is performed according to the Vienna scale.

  In the context of the present invention, anomalies are determined according to the Vienna scale. Thus, observing one or more of these abnormal categories of cells when assaying atypical as an optional extra marker in addition to the panel of markers of the present invention is an atypical marker in the analysis The fact that “abnormal” was found was recorded.

  An advantage of being able to assay atypical in addition to the four markers of the panel of the present invention is that an increase in sensitivity and / or specificity can be obtained.

  If any further assistance is needed, reference is made to a standard reference book in this area, such as Diagnostic Cytopathology 2nd edition by Winifred Gray. In addition or alternatively, reference books such as Gastrointestinal Pathology An Atlas and Textbook 3rd edition by Cecilia M. Fenoglio-Preiser, Amy E. Noffsinger, Grant N. Stemmermann, Patrick E. Lantz, Peter G. Isaacson may be used. . These references are specifically incorporated herein by reference with respect to the sections that describe the cell type characteristics referred to herein. Any other conventional cytology / histology guidance may also be used if necessary.

Hematoxylin and eosin (H & E)
Hematoxylin and eosin staining uses two separate dyes, one staining the nucleus and the other staining the cytoplasm and connective tissue. Hematoxylin is a dark purple-colored dye that stains the chromatin (nuclear material) in the nucleus to dark purple-blue. Eosin is an orange-pink-red pigment that stains cytoplasmic material including connective tissue and collagen and counterstains orange-pink. This counterstain acts as a sharp contrast with the purplish blue nuclear stain of the nucleus to help identify other objects in the tissue such as cell membranes (boundaries), red blood cells and body fluids.

  The staining process includes hydration of the sample (if necessary), staining and rinsing with a nuclear dye (hematoxylin), and counterstaining (eosin). These are rinsed, dehydrated if necessary (eg treated with water, then alcohol, then xylene) and prepared for observation, for example by adding a cover glass.

Progressive / regressive staining There are two methods for performing H & E staining. Put the slide in hematoxylin, then rinse and then in eosin, and the slide in a stronger form of hematoxylin, then in acid alcohol, take out hematoxylin from all but the nucleus and then differentiate, then eosin A regressive way to get inside. For both types of staining, the nuclei may be dyed dark blue with a bluing solution (Scott tap water or ammonia water).

  Progressive staining uses a milder form of hematoxylin, which stains only the nucleus of the cell and makes the nuclear material darker blue when rinsed with water. Using this method, the technician can simply dye, rinse, and move on to the next step. The advantages of this method are simplicity, fewer steps, and avoiding the possibility of over / under discrimination in acid alcohols. The level or color of staining is standardized and consistent. Progressive staining has the advantage that it is easier to automate.

  Hematoxylin products for progressive staining are commercially available, such as from Sigma (Sigma Aldrich) and include Gill No. 1, Gill No. 2, Gill No. 3 and Meyer's Hematoxylin. The difference between the three Gill stains is the intensity of hematoxylin. Since Gill No. 1 stains individual cells from body fluid suspensions rather than tissues, it is mainly used for cytological staining where weaker hematoxylin is appropriate. Gil's Nos. 2 and 3 are stronger and are commonly used for histological staining. These are being developed for organizational structures. The choice of using Gil No. 2 or No. 3 is a matter of preference for those skilled in the art.

  In retrograde staining, a stronger form of hematoxylin called Harris hematoxylin is used. Harris hematoxylin stains everything on the slide and is retained in the tissue when rinsed. Thus, the next step after staining and rinsing with water is to distinguish or remove excess hematoxylin from everything except the nucleus. As the slide is stirred in a mild acid alcohol solution, the acid alcohol solution slowly removes excess hematoxylin. After differentiation, the slides are rinsed and placed in a bluing solution (Scott's tap water or ammonia water), which results in a deep purple-blue nuclei.

  Hematoxylin products for retrograde staining are commercially available, such as from Sigma (Sigma Aldrich), and include Harris hematoxylin.

  After hematoxylin staining, the sample is rinsed and stained in eosin. If necessary, they can be dehydrated with a gradient alcohol, clarified in xylene, and finally prepared for observation using, for example, coverslips and / or permanent specimen mounting media. You can do it.

  Eosin products are commercially available, such as from Sigma (Sigma Aldrich) and include eosin Y, eosin Y alcoholic, eosin Y-phloxine. Similar to the staining of the three gils, eosin is distinguished by its intensity and color intensity. Eosin Y is the weakest of the three and stains cytoplasm and collagen pink. Eosin Y alcoholicity is a stronger dyeing and gives a brighter orange-red color due to its alcohol component. Eosin Y-Phloxine is the strongest stain and has an overwhelming red color due to the addition of Phloxine. Although the selection of eosin is by those skilled in the art, eosin Y-phloxin is generally considered too red for standard histology. Thus, suitably the eosin used is eosin Y alcoholic.

  It is an advantage of hematoxylin and eosin (H & E) staining that the use of molecular markers for certain cell types can be avoided.

Reference Standards The present invention requires the determination of the “abnormal” level of a marker. “Abnormal” may be defined by comparison with a reference standard.

  In the context of the present invention, the reference standard serves as the object of comparison, which can compare the expression level / methylation level / atypicality present in the sample of interest. The reference standard may include a sample from a healthy subject that is analyzed in parallel with the sample of interest. Alternatively, the reference standard may comprise an expression level value for the biomarker previously determined from a sample taken from a healthy subject to give a value for the expression level of the biomarker for comparison. . This has the advantage that it does not require parallel analysis of the reference sample each time the method is performed. Suitably, healthy individuals are individuals that are similar to the subject considered by demographic characteristics such as age, sex, weight and any other relevant parameters.

  The reference standard may be a set of expression level values as an average for the biomarker determined over time. This has the advantage of eliminating the practical problem of taking and measuring a sample from another individual each time the method is performed. Suitably, the set of expression level values as an average for the biomarkers determined over time is divided into different categories divided by medical characteristics such as age, gender, weight, etc. A more directly comparable set of values for the particular subject being examined can be provided.

  For the protein markers of the present invention, their staining is scored as described herein. The scoring system already considers normal / abnormal. Thus, the absolute categorization by scoring staining makes the need for a direct reference standard for each analysis advantageous.

  For methylation, the MethyLight score is considered abnormal when assessed as described herein as described in the Examples section.

  An exemplary methylation cutoff for use is 0.02604. This may vary depending on the needs of the operator implementing the present invention. For the Methylight assay, exemplary cutoffs (methylation cutoffs) range from 0.01 to 0.31. This may also vary depending on the needs of the operator implementing the present invention.

Reference sequence When referring to a specific amino acid residue using a numerical address, the numbering is done using the full-length amino acid sequence as the reference sequence. This is done as well as is well understood in the art to locate the residue of interest. This is not always an exact count, but the context should be noted. For example, if the protein of interest, such as human p53, is of slightly different length, the correct residue location in the p53 sequence corresponding to a particular residue will be the same number of the sequence of interest. Rather than simply choosing residues to have, it may be necessary to align the sequences and pick equivalent or corresponding residues. This is well within the scope of those skilled in the art.

  Furthermore, in the context of the present invention, it is important to detect specific polypeptide sequences corresponding to those described. Techniques and / or reagents for such detection are widely available and / or easy to obtain or make. Exemplary materials and techniques are given in the Examples section. The detection of a specific polypeptide, for example a polypeptide product of a specific gene, is suitably considered at the level of protein detection. This is not a determination of specific or precisely 100% identical amino acid sequences, but rather a problem of protein expression. Exemplary amino acid sequences are provided as guidance for the polypeptides to be detected and are not intended to limit the present invention to the determination of only those precise full-length 100% identical amino acid sequences. Thus variants such as allelic variants, point mutations that do not alter the basic identity of the polypeptide or variants such as short additions or deletions, or splice variants, fragments such as truncated or mature proteins, translation Post-modified proteins or other such general forms are considered within the scope of determining the presence / absence or level of expression of the various disclosed biomarker proteins.

  The fragment is suitably at least 10 amino acids long, suitably at least 25 amino acids, suitably at least 50 amino acids, suitably at least 100 amino acids, suitably at least 200 amino acids, suitably of the polypeptide of interest Mostly. Suitably, the fragment comprises the entire motif or domain of the polypeptide of interest.

Sequence homology / identity Sequence homology can be considered in terms of functional similarity (ie amino acid residues with similar chemical properties / functions), but in the context of this document, homology is It is preferably expressed in terms of identity.

  Sequence comparison can be performed visually or, more generally, with the aid of readily available sequence comparison programs. These publicly and commercially available computer programs can calculate percent homology (eg, percent identity) between two or more sequences.

  Percent identity may be calculated over contiguous sequences, i.e., aligning one sequence with the other sequence, each amino acid in one sequence with the corresponding amino acid in the other sequence, one at a time. Direct comparison of each residue. This is referred to as a “no gap” alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues (eg, less than 50 contiguous amino acids). For comparisons over longer sequences, gap scoring is used to obtain an optimal alignment and accurately reflect the level of identity in related sequences that have insertions or deletions relative to each other. A suitable computer program for performing such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, U.S.A; Devereux et al., 1984, Nucleic Acids Research 12: 387). Examples of other software that can perform sequence comparison include, but are not limited to, the BLAST package, FASTA (Altschul et al., 1990, J. Mol. Biol. 215: 403-410) and the GENEWORKS suite of comparison tools including.

  In this context, homologous amino acid sequences include amino acid sequences that are at least 40, 50, 60, 70, 80 or 90% identical. Most suitably, a polypeptide having at least 90% sequence identity to the biomarker of interest is considered to indicate the presence of that biomarker, and more suitably 95% or more at the amino acid level, or more A polypeptide that is suitably 98% identical is considered to indicate the presence of the biomarker. Suitably, the comparison is performed over at least the length of the polypeptide or fragment being assayed to determine the presence or absence of the biomarker of interest. Most suitably, the comparison is made over the entire length of the polypeptide of interest. The same considerations apply for nucleic acid nucleotide sequences.

advantage
Rugge, M., Fassan, M., Zaninotto, G., Pizzi, M., Giacomelli, L., Battaglia, G., Rizzetto, C., Parente, P., and Ancona, E. (2010). Aurora mRNA studies such as the main focus of kinase A in Barrett's carcinogenesis. Hum Pathol 41, 1380-1386 are difficult to establish "normal" levels. Defining a cutoff value is challenging. To make the result reliable, a very large sample size is required. A wide range of expression levels is observed. mRNA expression levels may not correlate with protein expression levels. mRNA can be degraded in samples collected with Cytosponge. The protein is more stable. Rugge et al does not mention the use of AURKA for the diagnosis of dysplasia in Barrett's esophagus. In the primary care environment, samples are collected, stored in the refrigerator, sent by mail, and finally arrive at the laboratory for testing. An advantage of the present invention is that the signal is not impaired during such sample processing. Rugge et al measures AKA by IHC and correlates with p53. The main drawback in Rugge et al is that AKA is reported as the primary cytoplasmic stain. This is very problematic because AKA functions in the nucleus and thus Rugge et al's cytoplasmic staining does not appear to be reliable. The Ab used by Rugge et al is from Epitomics, which is likely to produce non-specific and unreliable results. In contrast, we show nuclear staining. For example, we use antibodies from Millipore. The present inventors have confirmed the specificity of the antibody.

  Suitably mRNA is not used for analysis in the present invention.

  Suitably, the antibodies used in the present invention are specific for the protein being assayed.

  Liu et al 2008 is studying a panel of cancer from Chinese patients. In China,> 90% of esophageal cancer is squamous cell carcinoma. Thus, the authors demonstrate p53 expression in squamous cell carcinoma of the esophagus, but not with progression from Barrett's esophagus to adenocarcinoma.

  Agnese et al 2007 seeks to assess whether Aurora kinase A and p53 can help distinguish between Barrett's esophagus with intestinal metaplasia and Barrett's esophagus with gastric metaplasia. The conclusions in the summary state that the study is too small to get any significant result. In any case, in contrast, the present invention relates to the detection of dysplasia / cancer, for example in Barrett's esophagus, which is a separate issue from Agnese et al's attempt to distinguish between gastric metaplasia and intestinal metaplasia. It is. Agnese et al does not measure RNA transcript levels and examine protein levels of Aurora kinase A. RNA transcript levels are not necessarily interpreted as proteins due to post-translational modifications. We do not rely on RNA to say that this is a good protein level biomarker. A large number of candidate markers are dropped at this stage, ie do not yield good protein biomarkers.

  The invention will now be described by numbered paragraphs.

i. a method for assisting in detecting surface abnormalities of the esophagus
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3;
Detection of at least two abnormal levels of the marker means that the likelihood of a surface abnormality of the subject's esophagus is increased.

ii. Step (b)
(1) cells
(I) p53;
(Ii) c-Myc;
Contacting with a reagent for detecting at least a first molecular marker selected from (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3;
(2) The method according to paragraph i, comprising contacting the cell with a reagent for detecting at least a second molecular marker selected from (i) to (iv).

iii. In paragraph i or paragraph ii, wherein the surface abnormality is selected from the group consisting of mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and intramucosal carcinoma (IMC) The method described.

iv. The method of paragraph i or paragraph ii, wherein abnormal levels of at least three of the markers are assayed.

v. The method of any of paragraphs i-iv, wherein abnormal levels of at least four of the markers are assayed.

vi. The method of any of paragraphs iv, further comprising assaying the cells for atypical.

vii. The method of any of paragraphs i-vi, wherein the cells are recovered by unbiased sampling of the surface of the esophagus.

viii. The method of paragraph vii, wherein the cells are harvested using a capsule sponge.

ix. Before the cells are contacted with a reagent for detecting a molecular marker, (i) pelleting the cells by centrifugation; (ii) resuspending the cells in plasma; (iii) A method according to any of paragraphs i-viii, prepared by adding thrombin and incubating until a clot is formed.

x. The method of paragraph ix, further comprising incubating the clot in formalin, processing to paraffin blocks, and slicing into sections suitable for microscopy.

The method of any of paragraphs ix, wherein xi.p53 is assessed by immunohistochemistry.

The method of any of paragraphs i-xi, wherein xii.cMyc is assessed by immunohistochemistry.

xiii. The method of any of paragraphs i through xii, wherein AURKA is assessed by immunohistochemistry.

xiv. The method of any of paragraphs i through xiii, wherein methylation of MyoD / Runx3 is assessed by MethyLight analysis.

xv. The method of paragraph vi, wherein atypicality is assessed by scoring the cell for its morphology according to the Vienna scale.

xvi. The method of any of paragraphs i-xv, wherein the step of assaying the cells for TFF3 precedes step (b) of the method.

xvii. an assay for selecting a treatment regimen comprising:
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3;
An assay that selects an endoscopy and biopsy treatment regimen if at least two abnormal levels of the marker are detected.

xviii. (a) configured to analyze an esophageal sample from a subject, said analysis comprising:
(B) the cells
(I) p53;
(Ii) c-Myc;
A device or system comprising the step of assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3,
Including output module,
An apparatus or system wherein the output module indicates that the likelihood of a surface abnormality in the esophagus for the subject is increasing if at least two abnormal levels of the marker are detected.

xix. Use of a substance that recognizes, binds to or has affinity for a methylation of a polypeptide or a nucleic acid sequence for use in assisting in the detection of surface abnormalities in a subject's esophagus, Use wherein the peptide and / or nucleic acid sequence is as defined in any of paragraphs i-xv.

xx. Use according to paragraph xix of a combination of substances, each of which recognizes, binds to or has affinity for one or more of a polypeptide or nucleic acid sequence, respectively.

xxi. An assay device for use in assisting in the detection of surface abnormalities in a subject's esophagus, which contains a substance that recognizes, binds to or has affinity for the methylation of a polypeptide or a nucleic acid sequence An assay device comprising a solid substrate having a location, wherein the polypeptide and / or nucleic acid sequence is as defined in any of paragraphs i-xv.

xxii. (i) p53 in a biological sample;
(Ii) c-Myc;
(Iii) AURKA
And a reagent for determining the methylation level of MyoD and Runx3.

xxiii. A method for assisting in detecting a surface abnormality of a subject's esophagus, the method comprising providing a sample of cells from the subject, wherein the sample contains cells recovered from the surface of the subject's esophagus And assaying said cells for TFF3, wherein if TFF3 is detected in the cells of the sample, performing the method of any of paragraphs i-xv, and in addition to detecting TFF3 Detecting an abnormal level of at least one marker indicates that the likelihood of a surface abnormality of the subject's esophagus is increased.

xxiv. At least two markers in addition to detecting TFF3, preferably at least three markers in addition to detecting TFF3, preferably at least four markers in addition to detecting TFF3, preferably all five in addition to detecting TFF3 The method of paragraph xxiii, wherein detection of an abnormal level of a marker of said indicates an increased likelihood of a surface abnormality in the subject's esophagus.

xxv. The method of paragraph xxiii or paragraph xxiv, wherein the cells are harvested by unbiased sampling of the surface of the esophagus.

xxvi. The method of paragraph xxv, wherein the cells are harvested using a capsule sponge.

Embodiments of the present invention will now be further described with reference to the accompanying drawings. The drawings are as follows.
Shown is an example of c-MYC staining for cells obtained from Cytosponge ™ at four different staining intensities (0, 1, 2, 3). A photograph and a graph are shown. A flowchart is shown. A flowchart is shown. A flowchart is shown. Show photos. A flowchart showing the outline of the research is shown. The number of samples used at each stage is indicated. The method used for each study phase is shown on the left. EAC, esophageal adenocarcinoma, BE, Barrett's esophagus, HGD, advanced dysplasia. 3 shows mutations in esophageal adenocarcinoma. The upper bar graph shows the percentage of samples with abnormalities for the indicated genes. Bold numbers indicate the total number of mutations for each gene. Included genes with 4 or more mutations in our EAC discovery and validation cohort (a total of 112 patients combined). The percentage of missense, nonsense / splice and indel mutations is indicated. The lower matrix shows the number of samples with mutations in both genes for each potential gene pair. Boxes highlighted in red indicate significantly concurrent mutations (Benjamini-Hochberg adjusted p-value <0.05). The TP53 and SMAD4 mutations precisely define the boundaries of progression towards cancer, while other mutations are shown to occur at independent disease stages. A. Bar graph showing the number of dysplastic BE (NDBE, never-dysplastic BE) patients with at least one mutation, BE patients with high dysplasia (HGD) and EAC patients in our panel of 26 genes. B. Percentage of dysplastic BE, HGD with BE and EAC samples with mutations in the recurrently mutated genes identified in the EAC discovery and EAC validation cohorts (≧ 4 samples mutated). Only TP53 and SMAD4 are genes whose mutations divide the boundary between dysplastic and dysplastic BE (TP53) or cancer (SMAD4) ( ^* p <0.05). C. A proposed model for mutations that define boundaries in BE cancer development. The finely divided boxes indicate a number of other mutations that can occur and can provide selective benefits at any stage of the disease. FIG. 5 shows that TP53 mutation can be used to diagnose BE with common hyperplasia in Cytosponge ™. A. Schematic representation of Cytosponge ™ sampling of cells from the top of the stomach, the full length of the esophagus and the oropharynx. B. Allele fractions for known TP53 mutations previously identified by TP53 sequencing for diagnostic biopsies. For these four patients, mutations can also be detected in the material recovered using Cytosponge ™. Patient 4 swallows Cytosponge ™ over two different occasions 8 months apart and shows data for both Cytosponge ™ samples. N / A = not applicable since no sample was taken, AF = allele fraction. C. The allelic fraction of TP53 mutations identified in the Cytosponge ™ sample is shown for three patient groups: non-BE, BE without dysplasia and BE with high dysplasia (HGD). D. The location of the TP53 mutation identified for the Cytosponge ™ sample is shown above the gene diagram compared to that found in the EAC and BE HGD biopsy cohorts. The dotted line on the gene summary shows two small regions (amino acids 1-27 and 361-393) that are not covered by the multiplexed PCR assay. TA, transcription activation domain, OD, oligomerization domain.

  Further specific preferred embodiments are set out in the accompanying independent and dependent claims. The features of the dependent claims may be combined with the features of the independent claims, where appropriate, in combinations other than those explicitly stated in the claims.

Where a feature of a device is described as being operable to provide a function, this is recognized as including a feature of the device that provides or is adapted or configured to provide that function. Is done.
[Example]

Marker Selection There were several reasons for choosing the four molecular risk stratified biomarkers (and possibly the fifth atypical marker), examples of which are given below.

  p53 protein accumulation is one of the best characterized tumor suppressor proteins, p53, and dysplasia in Barrett's esophagus (Bian, YS, Osterheld, MC, Bosman, FT, Benhattar, J., and Fontolliet, C. (2001). P53 gene mutation and protein accumulation during neoplastic progression in Barrett's esophagus. Mod Pathol 14, 397-403) and increased risk of progression to OAC (Kastelein, F., Biermann, K., Steyerberg, EW) , Verheij, J., Kalisvaart, M., Looijenga, LH, Stoop, HA, Walter, L., Kuipers, EJ, Spaander, MC, et al. (2012) .Aberrant p53 protein expression is associated with an increased risk of neoplastic progression in patients with Barrett's oesophagus. Gut; Sikkema, M., Kerkhof, M., Steyerberg, EW, Kusters, JG, van Strien, PM, Looman, CW, van Dekken, H., Siersema, PD, and Kuipers, EJ (2009). Aneuploidy and overexpression of Ki67 and p53 as markers for neoplastic progression in Barrett's esophagus: a case-con trol study. Am J Gastroenterol 104, 2673-2680) and was selected as a biomarker.

  C-MYC, a well-characterized oncogene, is repeatedly amplified in OAC (Miller, CT, Moy, JR, Lin, L., Schipper, M., Normolle, D., Brenner, DE, Iannettoni, MD, Orringer, MB, and Beer, DG (2003). Gene amplification in esophageal adenocarcinomas and Barrett's with high-grade dysplasia. Clin Cancer Res 9, 4819-4825; Rygiel, AM, Milano, F., Ten Kate, FJ, Schaap, A., Wang, KK, Peppelenbosch, MP, Bergman, JJ, and Krishnadath, KK (2008) .Gains and amplifications of c-myc, EGFR, and 20.q13 loci in the no dysplasia-dysplasia-adenocarcinoma sequence of Barrett's esophagus. Cancer Epidemiol Biomarkers Prev 17, 1380-1385), included because it shows increased gene expression in Barrett's esophagus with highly dysplasia in our own gene expression array.

  Aurora kinase A (AURKA) was chosen as a surrogate marker for aneuploidy because it has been shown to be associated with AURKA overexpression, centrosome replication and aneuploidy. AURKA is an important regulator of mitosis initiation, centrosome maturation and spindle formation, and overexpression of AURKA has been shown to cause centrosome replication and chromosomal instability (Zhou, H., Kuang, J., Zhong, L., Kuo, WL, Gray, JW, Sahin, A., Brinkley, BR, and Sen, S. (1998). Tumour amplified kinase STK15 / BTAK induces centrosome amplification, aneuploidy and transformation. Nat Genet 20, 189-193). AURKA protein expression has also been shown to be significantly upregulated in Barrett's esophagus and OAC with high dysplasia compared to Barrett's esophagus without dysplasia (Rugge, M., Fassan, M. , Zaninotto, G., Pizzi, M., Giacomelli, L., Battaglia, G., Rizzetto, C., Parente, P., and Ancona, E. (2010). Aurora kinase A in Barrett's carcinogenesis. Hum Pathol 41 , 1380-1386).

  For methylation biomarkers, five genes previously tested to be methylated with increasing degree of dysplasia were tested. These genes were p16, ESR1, MYOD1, HPP1 and RUNX3 (Eads, CA, Lord, RV, Wickramasinghe, K., Long, TI, Kurumboor, SK, Bernstein, L., Peters, JH, DeMeester, SR, DeMeester, TR, Skinner, KA, et al. (2001). Epigenetic patterns in the progression of esophageal adenocarcinoma. Cancer Res 61, 3410-3418; Schulmann, K., Sterian, A., Berki, A., Yin , J., Sato, F., Xu, Y., Olaru, A., Wang, S., Mori, Y., Deacu, E., et al. (2005). Inactivation of p16, RUNX3, and HPP1 occurs early in Barrett's-associated neoplastic progression and predicts progression risk. Oncogene 24, 4138-4148). The best two were selected (MYOD1 and RUNX3).

Eliminating markers
There is a solid reason for eliminating other potential biomarkers for use with Cytosponge ™. Some examples of markers excluded from panel design are discussed below.

  Eleven other potential biomarkers were evaluated to determine if they could be used with Cytosponge ™ to detect Barrett's esophagus with dysplasia. Eleven biomarkers were EGFR, CDNK2A, FGFR2, CCNA1, DDX21, MSLN, PLK1, HER2, DNMT1, MYHFD2, and VNN2. EGFR, HER2, CDNK2A, CCNA1 and FGFR2 were selected from published literature, and DDX21, MSLN, PLK1, DNMT1, MTHFD2 and VNN2 were selected from in-house gene expression array data. VNN2 was excluded because there is no antibody available to stain formalin fixed paraffin embedded (FFPE) slides for this protein. FGFR2 and CDKN2A were excluded because both expression of these proteins was also detected in gastric gland tissue sampled by Cytosponge ™. MTHFD2 was excluded because the staining was only cytoplasm and was weak overall.

  CCNA1 has been successfully used as a biomarker in our laboratory (Lao-Sirieix, P., Brais, R., Lovat, L., Coleman, N., and Fitzgerald, RC ( 2004). Cell cycle phase abnormalities do not account for disordered proliferation in Barrett's carcinogenesis. Neoplasia 6, 751-760; Lao-Sirieix, P., Lovat, L., and Fitzgerald, RC (2007). Cyclin A immunocytology as a risk stratification tool for Barrett's esophagus surveillance. Clin Cancer Res 13, 659-665), Cytosponge ™, directly and initially tested. Unfortunately, CCNA1 does not work well with Cytosponge ™ in preliminary analysis (TFF3 + positive control without Barrett's esophagus = 26, NDBE = 44, uncertain for dysplasia = 12, LGD = 7, HGD = 7 Therefore, the BEST2 study was discontinued. CCNA1 failed most likely due to failure to determine compartment-specific growth (surface-deeper glands) from normal tissue growth and the structure of cells recovered with Cytosponge ™ .

  HER2 staining was tested on several Cytosponge ™ samples, but HER2 is known to be amplified or overexpressed only in about 15% of Barrett's esophagus with high dysplasia, so it is sufficiently sensitive Staining was stopped because it could not be a high biomarker.

  The remaining 5 biomarkers were excluded because they were not sufficiently sensitive or specific. See table.

Table: Sensitivity and specificity of five biomarkers that stained with our own TMA but did not remain until the final panel. The TMA consisted of a Barrett's esophageal biopsy with 54 dysplasias, a Barrett's esophageal biopsy with 32 mild dysplasias, and a Barrett's esophageal biopsy with 18 severe dysplasias.

  MSLN was excluded because it is expressed in Barrett's esophagus without dysplasia and is therefore not specific enough to detect Barrett's esophagus with dysplasia. Although DNMT1 appeared to be possible because it was very specific (98%), the data did not match when we tried to validate the data with a different DNMT1 antibody. Thus, we lost DNMT1 as a biomarker because we lost confidence in this antibody.

  EGFR was excluded because the overall sensitivity (72%) and specificity (77%) were too low. DDX21 was acceptable for sensitivity and specificity, but in many cases of Barrett's esophagus with low DDX21 expression and no dysplasia, we were looking for a clearer biomarker with no staining for staining So excluded. PLK1 had good sensitivity (91%) and good specificity (88%), but this biomarker showed better sensitivity (93%) and specificity (94%) data for AURKA, Since AURKA and PLK1 overexpression detected essentially the same case, they were excluded and we selected only one of the markers, which was selected because AURKA showed better data.

Sample processing and preparation Capsule sponge specimen processing
Cytosponge ™ capsules were swallowed by the patient and then immediately placed in a preservative solution at 4 ° C. until further processing. The sample was vortexed well and shaken vigorously to remove any cells from the sponge material. The preservative solution containing the cells was centrifuged at 1000 RPM for 5 minutes to pellet the cells. The resulting pellet was resuspended in 500 μL of plasma and thrombin (Diagnostic reagents, Oxford, UK) was then added in 10 μL increments until a clot was formed. The clot was then processed into a paraffin block after being placed in formalin for 24 hours. The sample was cut into 3.5 μm sections and two sections were placed on slides 1 and 2 to obtain 15 slides named slides 1-15.

Optional additional marker, atypical assay
Atypical evaluation of samples derived from Cytosponge is performed by microscopic examination and scoring.

  The first slide containing two sections was stained with H & E and atypical pathologists (Dr Maria O'Donovan) evaluated.

  Scoring is performed according to the Vienna scale.

Marker assays, protein biomarkers
Each of the three protein biomarkers on / in a cell in a sample obtained using Cytosponge ™ was assayed by immunohistochemical staining.

  For each protein biomarker, one slide was stained using immunohistochemistry (IHC) to assess protein expression in each of the samples. Slide 4 was used for p53, slide 8 was used for c-MYC, and slide 10 was used for AURKA.

  All slides were stained using a BondMax automatic stainer with a Leica Bond polymer detection kit. Conditions and antibodies used can be found in the table below.

  Suitably cMYC is stained using the MRC + E protocol, but the antibody is incubated for 60 minutes, suitably AURKA is stained using the MRC + E protocol, while the primary antibody is incubated for only 15 minutes. It should be noted that.

Scoring of immunohistochemical staining p53 was scored as 0-3 (intensity of staining), 3 was considered significant staining, 0, 1 or 2 was considered not significant staining. Only strong (intensity = 3) p53 staining was considered significant. p53 accumulation has been shown to correlate with Barrett's esophagus with dysplasia and also predict progression (Kaye, PV, Haider, SA, Ilyas, M., James, PD, Soomro, I., Faisal, W ., Catton, J., Parsons, SL, and Ragunath, K. (2009). Barrett's dysplasia and the Viennaclassification: reproducibility, prediction of progression and impact of consensus reporting and p53 immunohistochemistry. Histopathology 54, 699-712; Skacel, M ., Petras, RE, Rybicki, LA, Gramlich, TL, Richter, JE, Falk, GW, and Goldblum, JR (2002) .p53 expression in low grade dysplasia in Barrett's esophagus: correlation with interobserver agreement and disease progression. Gastroenterol 97, 2508-2513). Since epithelial cells in Barrett's esophagus are not frequently stained for p53, the absence pattern (Kaye, PV, Haider, SA, James, PD, Soomro, I., Catton, J., Parsons, SL, Ragunath, K., and Ilyas, M. (2010). Novel staining pattern of p53 in Barrett's dysplasia--the absent pattern. Histopathology 57, 933-935) was not considered significant.

  c-MYC was scored as 0-3 (intensity of staining), 0 and 1 were considered not significant staining, 2 and 3 were considered significant staining. This cut-off was chosen because it most usefully distinguished between Barrett's esophagus without dysplasia and Barrett's esophagus with any dysplasia. An example of c-MYC staining at different intensities is found in FIG.

  AURKA was scored as 0 or 1, where 0 was no staining and 1 was any positive staining. Examples of no staining and positive staining are shown in FIG.

  Suitably, AURKA staining is nucleus. Suitably, only nuclear staining is evaluated in the AURKA scoring. Suitably, cytoplasmic staining (if any) is ignored. Suitably, AURKA staining according to the present invention is not cytoplasmic.

Initial testing of the three protein biomarkers To perform further screening and ensure that the three potential protein biomarkers work well in our hands, p53, c-MYC and AURKA staining were It was carried out with its own Barrett's esophageal tissue microarray (TMA, tissue microarray). These TMAs consisted of Barrett's esophageal biopsy with 54 dysplasias, Barrett's esophageal biopsy with 32 mild dysplasias and Barrett's esophageal biopsy with 18 severe dysplasias. Since these TMAs consisted of Barrett's esophageal biopsy, only the surface staining, which is the cell that Cytosponge ™ would be sampling, was scored. In this data set, all three biomarkers performed well as can be seen from the table below.

Table of sensitivity and specificity of p53, c-MYC and AURKA in our own Barrett's esophageal TMA. TMA consisted of a Barrett's esophageal biopsy with 54 dysplasias, a Barrett's esophageal biopsy with 32 mild dysplasias and a Barrett's esophageal biopsy with 18 severe dysplasias:

  Thus, these confirmed markers were advanced and evaluated against cell samples collected using Cytosponge ™.

Marker assays, methylation markers
Methylation analysis on cells collected using Cytosponge ™ is performed as follows. Genomic DNA was extracted from 8 × 10 μm sections of treated Cytosponge ™ FFPE clots using deparaffinized buffer (Qiagen) and QIAamp FFPE DNA tissue kit (Qiagen). The protocol is the manufacturer except that the sample was incubated at 56 ° C. for 24 hours instead of the 1 hour described, and 10 μl of excess proteinase K was added to the sample after approximately half of the 24 hour incubation. Followed as described by. Following extraction, DNA was quantified using the Qubit ™ dsDNA HS assay kit (Invitrogen) and 75 ng of the EZ DNA methylation-Gold ™ kit (as described in the manufacturer). Used to convert to bisulfite. Samples were eluted in 25 μl water and Eads, CA, Danenberg, KD, Kawakami, K., Saltz, LB, Blake, C., Shibata, D., Danenberg, PV, and Laird, PW (2000). MethyLight: 2 μl per MethyLight reaction was used as described in Nucleic Acids Res 28, E32. β-actin was used as an internal control to normalize the amount of input DNA. The primer and probe sequences used were MYOD1 forward primer: 5'-gagcgcgcgtagttagcg-3 ', MYOD1 reverse primer: 5'-tccgacacgccctttcc-3', MYOD1 probe: 5'-6FAM-ctccaacacccgactactatatccgcgaaa-TAMRA-3 ', ACTB forward Primer: 5'-tggtgatggaggaggtttagtaagt-3 ', ACTB reverse primer: 5'-aaccaataaaacctactcctcccttaa-3', ACTB probe: 5'-6FAM-accaccacccaacacacaataacaaacaca-TAMRA-3 '(Eads, CA, Lord, RV, Wickramasinghe, K. Long, TI, Kurumboor, SK, Bernstein, L., Peters, JH, DeMeester, SR, DeMeester, TR, Skinner, KA, et al. (2001). Epigenetic patterns in the progression of esophageal adenocarcinoma. Cancer Res 61, 3410 -3418), RUNX3 forward primer from Meltzer laboratory: 5'-ggcttttggcgagtagtggtc-3 ', RUNX3 reverse primer: 5'-acgaccgacgcgaacg-3', RUNX3 protein: 5'-6FAM-cgttttgaggttcg ggtttcgtcgtt-TAMRA-3 ′. Using universal methylated DNA (D5010-1, Zymo Research) converted to bisulfite, a standard curve was derived for each of the primer and probe sets, and the calibrator was used in all experiments, in all samples. Allowed absolute quantification of methylation levels. The amplification conditions used for all reactions were 95 ° C. for 10 minutes, followed by 50 cycles of 95 ° C. for 15 seconds and 60 ° C. for 1 minute.

The degree of methylation for each gene was calculated using the following formula:
% Methylation = (A / B) / (C / D)
A = methylation value of the gene of interest B = methylation value of the gene of interest in the fully methylated control C = level of β-actin amplification in the sample D = level of amplification of β-actin in the fully methylated control

  The% methylation of the two genes was then added together to obtain a methylation value.

Initial test of methylated region 113 Cytosponge ™ samples (15 TFF3 + control without Barrett's esophagus, Barrett's esophagus with 54 dysplasia, Barrett's esophagus with 20 LGD and Barrett with 24 HGD In a preliminary experiment consisting of the esophagus), all five methylated regions (p16, HPP1, RUNX3, ESR1 and MYOD1) were evaluated and which subset of the methylated regions worked best, Cytosponge ™ The best sensitivity and specificity for detecting dysplasia was evaluated using the data shown in the table below.

Table showing the area under the curve (AUC) for five different methylation biomarkers. (15 TFF3 + control without Barrett's esophagus, 54 Barrett's esophagus without dysplasia, Barrett's esophagus with 20 LGD and Barrett's esophagus with 24 HGD):

  RUNX3 and MYOD1 together showed the best area under the curve when comparing any dysplasia to no dysplasia, so they were advanced and further evaluated in Cytosponge ™ samples.

Detection of Surface Abnormalities In this example, we demonstrate a method that assists in detecting surface abnormalities in a subject's esophagus.

  A sample of cells from the subject is provided. The sample includes cells recovered from the surface of the subject's esophagus. In this example, the cells were collected by swallowing and getting back the abrasive cell collection device. In this example, the device is Cytosponge ™. Thus, the cells were sampled from the surface of the subject's esophagus.

Cells,
(I) p53;
(Ii) c-Myc;
Assay for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3.

  Demonstrate the performance of risk stratified biomarkers against the BEST2 Cytosponge ™ sample. In this example, after selecting three protein biomarkers and a 2-gene methylation panel as in the previous example, all four risk stratified bios that may also include a fifth atypical marker. The marker was tested against a BEST2 Cytosponge ™ sample.

  The data presented in this example are from 18 control patients, 95 Barrett's esophageal patients without dysplasia, 25 Barrett's esophageal patients with LGD and 30 Barrett's esophageal patients with HGD.

  The lack of p53, c-MYC and AURKA staining in Barrett's esophagus without dysplasia and a markedly intense staining in Barrett's esophagus with dysplasia are shown in FIG. FIG. 2 shows a panel of markers for detecting dysplasia in samples collected from the surface of the esophagus, such as by using Cytosponge ™. The marker panel includes three protein biomarkers (p53, c-MYC and Aurora kinase A) and a two-gene methylation panel consisting of RUNX3 and MYOD1.

  When comparing Barrett's esophagus without dysplasia to Barrett's esophagus with HGD, p53, c-MYC and AURKA have a sensitivity of 57, 60 and 73%, respectively, and a specificity of 97, 89 and 85%, respectively. Indicates. The percentage of methylation of RUNX3 and MYOD1 when added together gave an area under the curve of 0.815 and a sensitivity and specificity of 83% and 80%, respectively, under “MethyLight” Shown in the table.

Table of sensitivity and specificity values for a panel of risk stratification markers when comparing Barrett's esophagus with advanced dysplasia and Barrett's esophagus without dysplasia:

  To assess the ability of this panel of risk stratification markers to detect dysplasia in Cytosponge ™ samples, a cutoff of at least two positive biomarkers was used. Using these criteria, 27/30 (90%) of patients with severe dysplasia were detected and 16/25 (64%) of patients with mild dysplasia were detected (see Table A below) Wanna)

  Table A shows how each risk stratification biomarker functions individually and whether dysplasia is detected in Cytosponge ™ when the panels are used together:

  These data gave 87% specificity when comparing high grade dysplasia to no dysplasia (ie Barrett's esophagus and controls without dysplasia).

  Thus, the detection of at least two abnormal levels of the marker is demonstrated to mean that there is an increased likelihood of surface abnormalities in the subject's esophagus.

Alternative approach, Cytosponge and single marker In this example, a method to assist in the detection of surface abnormalities in the subject's esophagus,
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus;
The sample of cells is collected using a swallowable abrasive device (eg Cytosponge ™) to sample the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least one marker selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3;
Detection of at least two abnormal levels of the marker means that the likelihood of a surface abnormality of the subject's esophagus is increased.

  In this example, the method steps are performed as in Example 7, but only one marker in the panel is required to be abnormal. This is therefore representative of the combination of the abrasive device / Cytosponge approach and the disclosed panel of markers.

  When the criteria were relaxed and one positive biomarker cutoff was used, 29/30 (97%) of advanced patients were detected and 23/35 (92%) of mild patients were detected (table above) See A). At this cutoff, the specificity is 59%. High sensitivity is essential for biomarker panels used for surveillance so as not to miss patients at risk of invasive cancer. Even a low specificity is still useful because a significant percentage of patients are spared unnecessary endoscopy.

Further Applications These data indicate that abrasive surface sampling (eg, using Cytosponge ™) and a panel of biomarkers can be used together to risk stratify BE patients. This has the advantage that the number of endoscopy required by BE patients can be reduced. This also has the advantage of avoiding sampling bias associated with biopsy. We propose that abrasive surface sampling (eg using Cytosponge ™) testing and a panel of risk biomarkers will change current clinical practices (and bring technical benefits over current clinical practices) (FIG. 3—Flowchart showing current clinical pathways for patients with persistent dyspepsia or reflux). Currently, patients who are symptomatic and experience persistent dyspepsia or reflux are suggested for endoscopy. If these patients are identified as having Barrett's esophagus, multiple biopsies are taken for pathological examination. Depending on the diagnosis, the patient enters a surveillance program and is suggested for endoscopy along with biopsy at determined time intervals. If Barrett's esophagus with severe dysplasia is detected, the patient is suggested for treatment.

  Since most patients with Barrett's esophagus do not progress at all and do not progress to Barrett's esophagus with dysplasia, these patients are endoscopically examined every two years, although the risk of progression is so low Have to endure.

  In accordance with the present invention, we combined these surveillance endoscopy coupled with biopsy with an abrasive surface sampling (eg, using Cytosponge ™) test and a panel of risk biomarkers described herein. It is proposed that the surveillance plan used in the project can be advantageously replaced. For example, this will be described with reference to FIG.

  FIG. 4 shows a flow chart showing a proposed clinical / screening pathway that includes abrasive surface sampling (eg, using Cytosponge ™) and a panel of biomarkers together. An exemplary number is included that indicates the number of endoscopy avoided by using Cytosponge ™ as a screening and / or risk stratification tool in accordance with the present invention. These numbers are based on a screening population of 10,000 and assume that 6.5% have Barrett's esophagus in the risk population. This number also assumes that 10% of patients with Barrett's esophagus have dysplasia. The number of patients at each stage depends on the accuracy (sensitivity and specificity) of the marker.

  FIG. 5 shows a flowchart illustrating the proposed Barrett's esophageal surveillance pathway, which includes an abrasive surface sampling (eg, using Cytosponge ™) and a panel of biomarkers. Include an exemplary number indicating the number of endoscopy avoided by using Cytosponge ™ as a risk stratification tool. This number also assumes that 10% of patients with Barrett's esophagus have dysplasia. The number of patients at each stage depends on the accuracy (sensitivity and specificity) of the marker.

  FIG. 6 shows an example of p53 staining intensity.

  Patients at high risk of having Barrett's esophagus (ie, patients with persistent reflux or dyspepsia) may experience a surface such as by swallowing a test described herein (eg, Cytosponge ™) as part of a screening program. Proposed to receive (by sampling).

  In one aspect, the sample may be pre-tested for the marker TFF3. If the test is negative for TFF3 (Barrett's esophageal biomarker), the patient is suggested to take the preliminary test again at defined intervals. Two negative Cytosponges ™ means that the subject has a very low risk of having Barrett's esophagus (approximately 0.2%), so there is no clinical reason for the patient to undergo endoscopy. Thus, in this case, risk biomarkers (ie, the test / panel of the present invention) may not be assayed on the patient's Cytosponge ™ sample. Patients may be retested in the future.

  However, in another embodiment, if any of the preliminary tests are positive for TFF3, a panel of risk biomarkers is used with an abrasive surface sample (eg, obtained using Cytosponge ™) according to the present invention. Do (assay). If none of the risk biomarkers in the panel described is positive, the patient is very unlikely to have any dysplasia (0.6%), so the patient is given 2 to 2 as part of a surveillance program. A retest during a period of 5 years may be proposed. If one or more of the biomarkers are positive, the patient is much more likely to have dysplasia (11.3%, a 19-fold higher relative risk than without a positive biomarker) Endoscopy associated with biopsy may be suggested. These numbers indicate that 56% (665/1184) unnecessary endoscopy is spared when abrasive surface sampling (eg, using Cytosponge ™) and a panel of risk biomarkers are combined. .

  Thus, the present invention provides significant technical and economic benefits as described herein.

Ordering mutations in the pre-invasive disease stage of esophageal cancer development This example demonstrates the use of p53 mutation analysis at the nucleic acid level. Furthermore, the use of SMAD4 as a marker for EAC is demonstrated.

Summary Cancer genome sequencing studies have identified a number of putative driving genes, but the relative timing of mutations in cancer development remains unknown. The slow progression from precancerous Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) provides an ideal model for studying somatic mutation sequencing. We identified genes that mutated repeatedly and assessed clonal structure using 112 EAC whole-genome sequencing and amplicon resequencing. We next observed 109 life from two important transition points in the development of malignant lesions: benign metaplastic dysplastic Barrett's esophagus (NDBE, n = 66) and severe dysplasia (HGD, n = 43). The test cohort was screened. Unexpectedly, the majority of genes that mutated repeatedly in EAC were also mutated in NDBE. Only TP53 and SMAD4 were stage specific and restricted to HGD and EAC, respectively. Finally, we used this finding to identify high-risk BE in a new non-endoscopic test. In conclusion, mutations in EAC-driven genes generally appear exceptionally early in disease progression and are deeply linked to diagnostic and therapeutic strategies.

Introduction Most epithelial cancers progress gradually from preinvasive lesions and in some cases, after initial metaplastic transformation. Research to characterize the genomic landscape of cancer focuses on established invasive disease with the goal of developing biomarkers for personalized treatment (Chin, L., Andersen, JN & Futreal, PA Cancer genomics: from discovery science to personalized medicine. Nat Med 17, 297-303 (2011)). However, extensive genomic heterogeneity has been shown to exist in the majority of advanced cancers (Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366, 883-92 (2012)). Thus, the most appropriate therapeutic targets are those mutations that occur early in disease progression and are clonal in the resulting malignant lesions. Identification of causative mutations that occur early in pathogenesis is also important for developing clinically useful biomarkers. In this relationship, disease stage boundaries, such as mutations that occur at the transition from non-dysplastic epithelium to dysplasia and then to cancer, are considered most informative. Proc Natl To date evidence for genetic evolution from precancerous lesions to cancer suggests that the accumulation of mutations is gradual (Jones, S. et al. Comparative lesion sequencing provides insights into tumor evolution. Acad Sci USA 105, 4283-8 (2008), Nik-Zainal, S. et al. The life history of 21 breast cancers.Cell 149, 994-1007 (2012), Vogelstein, B. et al. Genetic alterations during colorectal -tumor development. N Engl J Med 319, 525-32 (1988)). In the best studied example of adenoma-dysplasia-colorectal adenocarcinoma progression sequence, it was possible to assign timing for a limited number of candidate genes by comparative lesion sequencing (Jones, S. et al Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci USA 105, 4283-8 (2008)). More recent studies have used statistical algorithms to determine the life history of a tumor from a single sample (Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012), Vogelstein , B. et al. Genetic alterations during colorectal-tumor development. N Engl J Med 319, 525-32 (1988)).

  Esophageal adenocarcinoma (EAC) arises from the metaplastic Barrett's esophagus (BE) in the context of chronic inflammation that occurs following exposure to acid and bile (Goh, XY et al. Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.Gut 60, 1317-26 (2011), Quante, M. et al. Bile acid and inflammation activate gastric cardia stem cells in a mouse model of Barrett-like metaplasia. Cell 21, 36-51 (2012)). BE is well suited for genetic evolution studies by repeated mucosal sampling during clinical surveillance prior to therapeutic intervention (Greaves, M. & Maley, CC Clonal evolution in cancer. Nature 481, 306-13 ( 2012)). Previous studies of the EAC and BE have generally used a candidate gene approach with the aim of identifying clinical biomarkers to complement a difficult approach, histological examination (Greaves, M. et al. & Maley, CC Clonal evolution in cancer.Nature 481, 306-13 (2012), Varghese, S., Lao-Sirieix, P. & Fitzgerald, RC Identification and clinical implementation of biomarkers for Barrett's esophagus.Gastroenterology 142, 435-441 e2 (2012)). Data from high density single nucleotide polymorphism (SNP) arrays and exome sequencing studies are currently accumulating, with many mutations identified in many different genes (Dulak, AM et al. Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and ColonExhibit Distinct Patterns of Genome Instability and Oncogenesis.Cancer Res (2012), Dulak, AM et al.Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.Nat Genet 45 , 478-86 (2013)). However, few studies have yet focused on the precise ordering of these changes and associated clinical follow-up data in a large cohort of patients with precancerous disease.

  Recently, Agrawal et al. Performed exome sequencing on 11 EAC samples and 2 samples of BE adjacent to the cancer. Interestingly, the majority of mutations were found to be clearly present even in normal BE, as observed in colorectal adenocarcinoma (Agrawal, N. et al. Comparative genomic analysis of esophageal adenocarcinoma and squamous cell carcinoma. Cancer Discov (2012)). This raises the possibility that mutations that predict the risk of progression may be detectable in benign tissue by cytology prior to progression to malignant lesions. However, it is unclear how much the same mutation can be present in BE tissue from patients who have not progressed to cancer. This question is important. This is because the majority of patients with BE do not progress to cancer and somatic changes that occur early before dysplasia may not provide clinically distinct biomarkers. Biomarker research in this area is important. Because current endoscopic surveillance strategies are increasingly recognized as ineffective (Corley, DA et al. Impact of Endoscopic Surveillance on Mortality From Barrett's Esophagus-Associated Esophageal Adenocarcinomas. Gastroenterology 145, 312-319 e1 (2013)), so a new approach is needed (Shaheen, NJ & Hur, C. Garlic, Silver Bullets, and Surveillance Upper Endoscopy for Barrett's Esophagus. Gastroenterology 145, 273-6 ( 2013), Hayes, DF et al. Breaking a vicious cycle. Sci Transl Med 5, 196cm6 (2013)).

  The purpose of this study was 1) to identify a list of candidate new and repetitively mutated genes in the EAC, and 2) to accurately elucidate the stage of the disease in which the mutation occurs, and thus the role of these recurrent mutations in cancer progression 3) to test their usefulness in clinical applications using Cytosponge ™, a non-invasive, non-endoscopic cell sampling device.

Results High mutation load and unusual mutation signature in the EAC The discovery cohort (22 EACs subjected to WGS) was male dominant (M: F, 4.5: 1), mean age of 68 years (range 53-82) , And the majority reflected the known clinical demographic characteristics of the disease as advanced disease (81.8% (18/22)> stage I). 17 out of 22 (77.3%) cases had evidence of BE in the resected specimen (Table 1).

  Samples were sequenced to 63 and 67-fold average coverage in tumor and normal samples, respectively.

  We identified a median of 16,994 somatic SNVs (range: 4,518-56,528) and 994 small indels (range 262-3573) per sample. From this final data set, a total of 1,086 coding region mutations were subjected to validation as part of a larger pipeline benchmark evaluation study. We achieved a median coverage of> 13,000 times using ultra-deep targeted resequencing and confirmed 1,081 (99.5%) as somatic cells. Using Sanger sequencing, 23/25 (92%) of indel was indeed confirmed as a somatic cell. As observed by Dulak et al during the intervening time since the beginning of our study (Dulak, AM et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet 45, 478-86 (2013)), the most frequent mutation type across the discovery cohort was T: A> G: C transversion, with significant enrichment in CTT trinucleotides. This enrichment for T: A> G: C transversion is demonstrated in breast cancer, colorectal cancer and hepatocellular carcinoma (Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-93). (2012), Fujimoto, A. et al. Whole-genome sequencing of liver cancers identify etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet 44, 760-4 (2012), Bass, AJ et al. Genomic sequencing Nat genet 43, 964-8 (2011)) including other colorectal adenocarcinomas identify a recurrent VTI1A-TCF7L2 fusion. Distinguish EAC from other cancers studied by WGS.

Targeted amplicon resequencing in a validation cohort of EAC To identify novel genes involved in the development of EAC in BE, we identify recurringly mutated targets in our discovery cohort (n = 22 cases) Tried to do. Select a final list of 26 genes that are significantly mutated above the background rate or in the pathway of interest, and in a larger cohort (90 additional EACs, Table 1) using targeted amplicon resequencing Tested. Results include previous studies from our discovery cohort and others (Dulak, AM et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent), including identification of repetitive mutations in SWI / SNF complexes such as ARID1A driver events and mutational complexity. Nat Genet 45, 478-86 (2013), Agrawal, N. et al. Comparative genomic analysis of esophageal adenocarcinoma and squamous cell carcinoma. Cancer Discov (2012), Streppel, MM et al. Next-generation Sequencing of endoscopic biopsies identified ARID1A as a tumor-suppressor gene in Barrett's esophagus. Oncogene (2013)) was confirmed and expanded. Analysis of loss of ARID1A protein expression by immunohistochemistry in an additional EAC cohort of 298 identified absence or reduction of expression at 41% (122/298). This suggests that there may be an alternative mechanism of down-regulation, but we did not identify any large-scale structural variants within the WGS data from our discovery cohort (data not shown) .

  We then combined the data from both the discovery and validation cohorts and identified 15 genes that were mutated in 4 or more samples (Figure 8). These included those previously identified as EAC candidate genes and several new candidates MYO18B, SEMA5A and ABCB1. TP53 was mutated in the majority of cases. However, 31% of cases are wild type for TP53. We do not have sufficient ability to detect mutually exclusive mutations in our cohort, but we can detect significantly co-occurring mutations. The SEMA5A and ABCB1 mutations generally appeared in the same tumor than expected by chance (Benjamini-Hochberg adjusted p-value = 0.0021), but the reason for this association remains unknown.

Similar mutation frequency across the Barrett's esophageal disease stage The stage specificity of the mutation can be derived from patients at different stages of BE cancer development. Mutations that appear at disease stage boundaries may be candidate biomarkers of malignant progression. Furthermore, mutations that appear early in disease progression are ideal targets for new therapeutic interventions because they are present in the majority of more advanced lesion cells due to early clonal expansion of natural history It should be. Thus, we attempted to identify mutational status of 26 genes in our panel in BE samples obtained from a prospective cohort of patients undergoing endoscopic surveillance. This included 109 BE biopsies from 79 patients (FIG. 7). We have 66 anaplastic BE samples from 40 BE patients with no evidence of progression to dysplasia or malignancy (median follow-up time 58 months, range 4-132), and progression of invasive EAC 43 BE biopsy samples (from 39 patients) with histopathologically confirmed high dysplasia (HGD), which was the stage just before, were selected (Table 1). We did not include mild dysplasia because of poor agreement with the histopathological grading of this lesion (Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of Genetric Cancer. Nat Genet 43, 1219-23 (2011)).

  The results were striking and unexpected. For the anaplastic BE cohort, 21/40 (53%) patients were found to have mutations within their BE segment (FIG. 9a) and some biopsies contained multiple mutations . In total we identified 29 SNVs and 7 indels within this cohort. Importantly, mutations identified in anaplastic BE include ESMA (Dulak, AM et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events, including SMARAC4, ARID1A and CNTNAP5 (FIG. 9b). Nat Genet 45, 478-86 (2013), Curvers, WL et al. Low-grade dysplasia in Barrett's esophagus: overdiagnosed and underestimated. Am J Gastroenterol 105, 1523-30 (2010)) and other cancers ( Wang, K. et al. Exome sequencing identify frequent mutation of ARID1A in molecular subtypes of gastric cancer.Nat Genet 43, 1219-23 (2011), Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228-31 (2010)) occurred in several genes previously identified as driving factors. Interestingly, seven of these 29 SNVs were mutations at T: A base pairs. Of these, 5/7 (71%) occurred in TT dinucleotide sequences, and the mutational relationship was identified to be highly enriched in the EAC WGS data. Thus, this mutation process can be active even at the earliest stages of the disease. Of the 43 HGD biopsy samples, 39 (91%) were found to have at least one mutation of the gene in our panel with a total of 67 SNVs and 7 indels. Thus, rather than increasing the frequency of mutations in a given gene over the disease stage, we found that for the majority of genes, the mutation frequency did not differ significantly between anaplastic BE, HGD and EAC. Observed (Fischer's exact test with Benjamini-Hochberg correction for multiple tests, FIG. 9b). Only TP53 (p <0.0001) and SMAD4 (p = 0.0001) (FIGS. 9b and c) show the mutation frequency that distinguishes between disease stages and thus identifies progression towards malignant lesions. TP53 was found to be mutated repeatedly in both HGD (72%) and EAC (69%) samples, but only a single case (2.5%) in anaplastic BE. . SMAD4 was mutated at a lower frequency (13%) and was interestingly found only in the EAC, the invasive stage of the disease.

Clonal analysis of repetitive mutations Identifying the appearance of mutations at the earliest stages of disease progression, we then identified that these mutations were completely clonally or in our original discovery cohort of 22 EACs An attempt was made to identify whether it was subclonal. For each of the 15 genes mutated in ≧ 4 samples from our extended cohort, we combined SNV high-depth pro-sequencing, copy number variant data, and LOH analysis to identify tumor cells containing the mutation. The fraction was determined. If the mutation occurs at the earliest stage of disease progression, before the clonal expansion of the malignant lesion, we expect the mutation to be present in all cells of the tumor. This was the case for 7/15 genes, SMAD4, TP53, ARID1A, SMARAC4, TLR4, CDKN2A and PNLIPRP3. Mutations in the other eight genes (MYO18B, TRIM58, CNTNAP5, ABCB1, PCDH9, UNC13C, and CCDC102B) were not always present in major clones, and mutations in these genes occurred at multiple stages of tumorigenesis. (Fig. 9d).

Application of knowledge about sequencing of mutations to diagnostic trials Current clinical strategies for patients with BE are routine insights to try to identify patients with dysplasia who are at high risk for progression to adenocarcinoma Includes mirror examination. This approach is very controversial due to the inherent difficulty in accurately identifying dysplastic lesions, and recent data suggest that BE's endoscopic surveillance is ineffective (Corley, DA et al. Impact of Endoscopic Surveillance on Mortality From Barrett's Esophagus-Associated Esophageal Adenocarcinomas.Gastroenterology 145, 312-319 e1 (2013); Reid, BJ, Li, X. time for a new synthesis. Nat Rev Cancer 10, 87-101 (2010)). Difficulties associated with endoscopic surveillance for BE include sampling bias inherent in random biopsy protocols and subjective and time-consuming histopathological diagnosis of dysplasia. We have therefore developed a new approach that has the potential to overcome these limitations of BE surveillance. Strategies include a non-endoscopic device called Cytosponge ™ that can be provided to patients in a primary care environment. This device recovers cells from the entire esophageal mucosa, thus avoiding sampling bias and can be combined with objective biomarkers for diagnosis (Kadri, SR et al. Acceptability and accuracy of a non-endoscopic screening test for Barrett's oesophagus in primary care: cohort study.BMJ 341, c4372 (2010), Lao-Sirieix, P. et al. Non-endoscopic screening biomarkers for Barrett's oesophagus: from microarray analysis to the clinic.Gut 58, 1451- 9 (2009)). To date, we have focused on biomarkers for diagnosing BE, but since most BE patients do not progress to EAC, this BE biomarker can be used to identify high-risk dysplastic patients. It needs to be combined with a biomarker (or a panel of biomarkers). From the above sequencing data, the TP53 mutation meets the criteria for a good risk stratification candidate marker. This is because the TP53 mutation distinguishes between patients with and without advanced dysplasia, an important aspect of therapeutic intervention. Although the device samples abnormal tissue, the majority of cells recovered are from normal gastric gland tissue from the top of the stomach and the normal squamous epithelial region of the esophagus, so any mutant DNA is theoretically a minority. Yes and requires a very sensitive assay (Figure 10a). This situation is similar to detection of tumor cell free DNA in blood as a biomarker in advanced malignancy. Sensitive assays have been developed to detect very low levels of mutant DNA against normal background (Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA Sci Transl Med 4, 136ra68 (2012), Dawson, SJ et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 368, 1199-209 (2013)). We therefore took a similar approach to detect mutations in Cytosponge ™ material.

  To determine whether mutations within BE lesions can be detected in material recovered from Cytosponge ™, we first tested mutations previously identified in endoscopic BE biopsy. Four patients with HGD dysplasia had TP53 mutations and also swallowed Cytosponge ™ (patient 4 twice). For all four patients, a specific TP53 mutation was detected with an allele fraction (percentage of variant reading) between 0.04 and 0.24 (Figure 10b).

  We then tested whether we could detect an unknown TP53 mutation in the material collected using Cytosponge ™ as required by clinical trials. We amplified the majority of the coding region of TP53 (1019/1182 bp (86%)) by multiplex PCR and sequenced the amplified DNA by massively parallel sequencing. TP53 mutations are expressed in TAm-Seq (Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by samples from control patients (no BE), BE patients without dysplasia, and BE patients with severe dysplasia. It was called de novo using Sci Transl Med 4, 136ra68 (2012)). As we expected, TP53 mutations were not identified in samples from control patients or BE patients without dysplasia (FIG. 10c), in distinguishing between patients with HGD and those without dysplasia. 100% specificity was demonstrated. In contrast, TP53 mutations were identified in 19/22 (86%) HGD patients. Although the allelic fraction of TP53 mutations varied widely (between 0.006 and 0.357), anything within this range could be successfully called, and the mutation was almost clustered within the DNA binding domain as expected. (FIG. 10d).

DISCUSSION BE is the only known EAC precursor lesion and co-occurs in> 80% of cases with de novo (Theisen, J. et al. Preoperative chemotherapy unmasks underlying Barrett's mucosa in patients with adenocarcinoma of the distal esophagus Surg Endosc 16, 671-3 (2002)), but the majority of BE patients never progress to invasive disease (Bhat, S. et al. Risk of malignant progression in Barrett's esophagus patients: results from a large population -based study. J Natl Cancer Inst 103, 1049-57 (2011)). Thus, there is a need for sensitive and specific biomarkers that can identify patients at risk of progression. As early as the Nowell hypothesis, it was hypothesized that stepwise selection of genomic mutations was necessary for cancer progression (Nowell, PC The clonal evolution of tumor cell populations. Science 194, 23-8 (1976)). Somatic cell genomic variants should therefore be highly specific markers of disease stage sensitivity. By screening our panel of recurrently mutated genes in a cohort of BE patients who have never progressed to dysplasia and a cohort of patients with HGD, we have identified mutations across these disease stages. We wanted to identify the staged accumulation. Surprisingly, we have identified a number of mutations that occur with detectable allele fractions (> 10%) in anaplastic BE. Interestingly, the most common genetic mutations in EAC were also present at similar frequencies in BE and HGD samples, including mutations in cancer-related genes such as ARID1A and SMARAC4, which are members of the SWI / SNF complex . These data demonstrate a view of complex mutations that can exist even in tissues with a completely benign histopathological appearance and a very low risk of malignant progression. The exact role of these mutations at this early stage of disease progression remains unclear. However, clonal enhancement is known to occur frequently in BE, and these mutations do not lead to destruction of epithelial structures or provide the cellular features necessary for invasion It is possible to increase the degree. Similar observations have been reported for endometrial cancer. In the normal population, approximately 35% of women have PTEN mutant glands in endometrial tissue, but the lifetime risk of endometrial cancer is approximately 2.5% (Mutter, GL et al. Molecular identification of latent precancers in histologically normal endometrium. Cancer Res 61, 4311-4 (2001)).

  Our results have substantial implications for the specificity of tests aimed at using mutation-sensitive detection for early diagnosis of malignant lesions (Maley, CC et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet 38, 468-73 (2006)). Biomarkers that predict individuals who are at risk for cancer need to have substantial predictive power to distinguish between those who progress to cancer and those who do not progress to cancer. In our study, almost all of the genes that mutate repeatedly in the EAC, including ABCB1, CNTNAP5, and MYO18B, are excluded from being used as surveillance tools for progression risk. Only mutations in TP53 and SMAD4 precisely defined the boundaries of the disease state. The fact that the SMAD4 mutation was found only in EAC indicates a clear genetic difference between EAC and HGD. However, due to the low frequency of SMAD4 mutations (13%), this is less than optimal as a candidate for biomarker development. Moreover, rather than the EAC, the HGD is now an ideal clinical intervention point with the advent of endoscopic treatment. Thus, we focused on TP53 for Cytosponge (TM) studies of proof of principle. Sequencing techniques are currently being introduced for routine clinical use, and the gene of interest can be sequenced quickly, with excellent sensitivity, giving a quantitative readout (Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4, 136ra68 (2012)). We have detected mutations in 86% HGDCytosponge ™ samples using a simple and clinically usable test. In order to improve the sensitivity of any early detection program, it is also important to identify genetic or epigenetic changes that drive HGD and EAC in a minority of patients who do not have a detectable TP53 mutation. In addition, since genetic diversity has been shown to predict progression to BE, somatic mutation studies that look at both the presence and relative proportion of mutations in a panel of genes have been performed to identify patients with high-risk disease. It may also be possible to identify (Maley, CC et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet 38, 468-73 (2006)).

  In conclusion, anaplastic BE has frequent mutations that affect recurrently mutated genes in the EAC. In view of the low rate of progression to malignancy in anaplastic BE, the role of these mutations in the path to malignancy is unclear. It is generally accepted that the mutations observed in tumors occur in a linear progression and that each step brings the clone closer to the invasive endpoint. Our observation of mutations in almost all recurrently mutated genes in the tissues of patients who have not progressed to malignant lesions contradicts the major role of these mutations in progression towards cancer. Their repetitive nature suggests a role in clonal expansion at the precancerous stage, but these do not appear to result in a long-term increase in the likelihood of malignant lesion progression.

  From a clinical point of view, the majority of recurrently mutated genes in the EAC do not distinguish between the pre-cancerous and malignant stages of the disease, so they are simply mutated or non-mutated as biomarkers of malignant progression. Cannot be used for such two-way tests. Cytosponge (TM) provides a representative sample of the entire esophageal mucosa and can be coupled with high-throughput sequencing to enable sensitive and objective detection of HGD. This approach can be easily adapted as our understanding of the genetic basis of the disease progresses. In addition, our systematic molecular approach to identify key mutations involved in distinguishing preinvasive disease from invasive disease has applicability to other epithelial cancers that follow early detection.

Method Sample collection, pathological examination and extraction.
The study was approved by the institutional ethics committee (REC N 07 / H0305 / 52 and 10 / H0305 / 1) and informed consent was obtained from all patients individually. For the discovery cohort, patients with esophageal adenocarcinoma (EAC) were prospectively employed and samples were obtained from either surgical resection or endoscopic ultrasound (EUS). A normal squamous esophageal sample at least 5 cm away from the blood or tumor was used as a germline reference. All tissue samples were immediately frozen in liquid nitrogen immediately after collection and stored at -80 ° C. Prior to DNA extraction, one section was cut from each esophageal tissue sample and subjected to H & E staining. The cancer samples were considered suitable for DNA extraction only after consensus studies where two skilled pathologists confirmed tumor cell solidity ≧ 70%. If blood was not available, the same study process was applied to normal esophageal samples to ensure that only squamous epithelium was present. For the discovery cohort, 127 cases were screened from two institutions (Cambridge and Southampton). 63 cases have 70% cellularity required to meet ICGC criteria, of which 22 tumor: normal pairs are of sufficient quality and quantity of extracted DNA (total yield ≧ These were subjected to whole genome sequencing. From the remaining 105 available cases, 90 had> 50% cellularity and all of these had sufficient DNA for amplicon sequencing. For all cases in the discovery and validation cohorts, the 260/280 ratio was 1.8-2.1. For the pre-invasive disease cohort, we screened our entire 10-year predicted Barrett's esophageal cohort of> 500 patients, freezing material was available, and by examining frozen sections, after histopathological review of the skilled person Cases with homogeneous grade dysplasia were selected. All Cytosponge ™ samples were available as part of a temporary analysis from an ongoing prospective case-control study (BEST2).

  DNA was extracted from frozen esophageal tissues using the DNeasy kit (Qiagen) and from blood samples using the Nucleon ™ Genome Extraction Kit (Gen-Probe) according to the manufacturer's instructions. For verification, DNA was extracted using the AllPrepDNA / RNA mini kit (Qiagen) according to the manufacturer's instructions.

Whole Genome Sequencing Created a single library for each sample, under contract by Illumina to 100 bp paired end sequencing to a typical depth of at least 50 × where 94% of known genomes are sequenced to at least 8 × coverage And achieved a PHRED quality of at least 30 for at least 80% of the mapped bases. Typically, five lanes of the HiSeq-2000 (Illumina) flow cell achieved this, but some exceeded these minimum standards by a large difference since the samples were not multiplexed. The filtered read sequence is converted into a Burrows-Wheeler Alignment (BWA) (Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60 (2009 )) To the human reference genome (GRCh37) and the overlap was marked using Picard (https://picard.sourceforge.net). As part of the extensive quality assurance process, QC metrics and alignment statistics were calculated for each lane. The integrated QC for each discovery cohort sample was determined. Details of any tiles in the flow cell that were removed after QC were determined.

  Use the FastQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to assess the distribution of quality scores for sequencing reads and trim by degradation in quality during the second half of sequencing 3 lane sequencing that required

WGS mutation call SomaticSniper V1.0.2 that operates somatic single nucleotide variant (SNV) with the following command (Larson, DE et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 28, 311-7 (2012)):
somaticsniper-q1-Q15-Fvcf-J-r0.001000-T0.850,000 -N2-s0.01-f

Discovery applied from SomaticSniper and then applied to SomaticSniper and VarScan 2 (Koboldt, DC et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22, 568-76 (2012)) Using the following criteria derived from the comparison of genetic filters, Koboldt et al (Koboldt, DC et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22, 568-76 ( 2012)) and a custom script (homopolymer filter).
1. Germline and tumor sample coverage ≧ 10
2. 2. Average variant position in reading between 10th and 90th position Percentage of support readings from each chain ≧ 1% and ≦ 99%
4). Total support reading ≧ 4
5. Mean distance of variant bases from the effective 3 ′ end of support reading ≧ 20 bp
6). Difference in average mapping quality between reference support reading and variant support reading <30
7). Mean difference in length of trimming sequence between reference reading and variant reading <25 bp
8). Difference in total mismatch quality between reference reading and variant reading <100
9. Adjacent homopolymer <5 bp
10. Nearest indel ≧ 40 bp

  In addition, all variants were compared to dbSNP129 and removed if they overlap with the expected germline SNP. The median 99.7% of mappable genomes were defined as callable because they covered at least 10-fold coverage in tumors and matched germline samples.

  Candidate somatic cells indel were obtained from SAMtools (Li, H. et al. The Sequence Alignment / Map format and SAMtools. Bioinformatics 25, 2078-9 (2009)) and Pindel (Ye, K., Schulz, MH, Long, Q. , Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-71 (2009)) Adopted and filtered to exclude indels present in any matching normal genome of any of the 22 samples (including non-consensus indel calls). The indels that entered the coding region and splice sites were manually inspected to create a final list of calls. Variants were annotated with sequence ontology terms to indicate the results and position for Ensembl gene annotation. SNV and indel annotated with matching or closest features in UniSNP.

Validation of indel variants by PCR A total of 25 coding indels confirmed by manual review were randomly selected for validation. Primers (sequences are available upon request) were amplified to amplify the predicted variant locations. PCR was performed on both tumor and normal DNA, and the resulting product was Sanger sequenced. All traces were visualized using Chromas lite 2.01 and manually examined for the presence of variants. An indel was considered somatic if it was present only in the tumor signature.

Validation of single nucleotide variants by targeted resequencing As part of performing a larger benchmark evaluation of our SNV calling pipeline, we chose to validate the 2007 SNV. These SNVs did not pass the filter and included those predicted using the Illumina pipeline, ELAND alignment and STRELKA. A complete analysis of these data is ongoing and the overall objective is to optimize the sensitivity of our SNV calling pipeline. After a comparison of the preliminary analysis and the performance of the ICGC benchmark evaluation, we chose to increase the rigor of our filter for this preliminary data set (detailed above). The verification data in this document is only for SNVs that pass these additional filters. A putative non-synonymous SNV (1330 in total) received ultra-deep targeted sequencing. For 8 samples, all non-synonymous variants were sent for validation. In the remaining 14 cases, selected SNVs were limited to non-synonymous variants in genes that mutated in more than one sample. Amplicons are created, indexed, pooled and library according to Shah et al (Shah, SP et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486, 395-9 (2012)). Built. Samples were pooled separately and single lanes of HiSeq-2000 data were generated for each, leading to a typical depth of 13,855 coverage (IQR for amplicons: 3,408-39,059). Of these, for 1086, ≧ 50-fold coverage was generated for both tumor and normal. If the variant allele frequency is ≦ 1% in the matched normal and ≧ 2% in the tumor, the SNV is confirmed to be somatic, and 1081 SNVs meet these criteria, 1081/1086 A confirmation rate of (99.5%) was obtained.

Mutation validation in independent samples Mutation validation was performed with 90 additional EACs and 109 BEs, including 43 biopsy with histopathologically confirmed HGD and 66 biopsy without dysplasia. Performed in a biopsy cohort. An Access Array microfluidic PCR platform (Fluidigm) and high-throughput sequencing (Illumina) were used together for targeted resequencing.

  Amplicons with a median size of 180 bp (range 100-200 bp) were prepared using proprietary software from Fluidigm (primers are available upon request) (Forshew, T. et al. Noninvasive identification and monitoring of cancer It was designed using mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4, 136ra68 (2012)). After two iterations of primer design, one gene remained uncovered by the appropriate amplicon (DIRC3), which was removed from further analysis. Therefore, a total of 26 genes were selected. All primers were synthesized with a universal sequence (referred to as CS1 and CS2) attached to the 5 'end.

  Target amplification and barcode addition to the samples were performed using the manufacturer's standard multiplexing protocol (Fluidigm, Access Array User Guide). Primers were combined in a multiplexed pool ranging from 1-12 primer pairs. Using the Access Array system, PCR reagents (FastStart high fidelity PCR system, Roche), 47 DNA samples (50 ng) + single negative control and 48 sets of multiplexed primers, 2,304 unique 35 nL PCR reactions Combined with liquid. A thermal cycle was then performed to amplify all targets selected by PCR. After PCR, 48 multiplexed reaction amplification products were collected per sample using the collection reagent through the sample inlet for subsequent sequencing. Illumina sequencing adapter and 10 bp sample specific barcode were combined by an additional 15 cycles of PCR. After adding a barcode to the PCR product, the PCR product and water control from a small number of samples were analyzed using the Agilent 2100 BioAnalyzer to obtain the expected amplicon size and throughout the PCR reaction. Ensured that there was no contamination. These were then pooled together and purified using AMPure XP beads using a 1.8: 1.0 bead to amplicon ratio. The library was quantified using an Agilent BioAnalyzer and subjected to Illumina cluster generation. 100-150 bp paired end sequencing with 10 base indexing using custom sequencing primers targeting CS1 and CS2 tags for both Read 1, Read 2 (Index Read) and Read 3 according to manufacturer's recommendations (Barcode) Reading was performed with aHiSeq 2000 or MiSeq.

  Methods used for analysis of targeted sequencing data generated using TAm-Seq have been reported previously (Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4, 136ra68 (2012)). The reading was demultiplexed with a known list of barcodes that allowed zero mismatch. Each set of readings is independent of the hg19 reference genome using BWA in paired-end mode (Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60 (2009)) And aligned. Using the expected genomic location, each set of aligned reads was further separated into its constituent amplicons. For each amplicon SAMtools vl. 17 (Li, H. et al. The Sequence Alignment / Map format and SAMtools. Bioinformatics 25, 2078-9 (2009)). The observed frequency of non-reference alleles for all sequenced loci across all amplicons and barcodes was calculated using a 30 base quality and mapping quality cut-off. For each locus and base, the distribution of non-reference background allele frequency / reading was modeled and the probability of obtaining the observed frequency / number of readings (or more) was calculated. A putative substitution was identified based on a probability cut-off (edge of confidence interval) of 0.9995. The region covering the known SNPs and amplification primers obtained from the 1000 Genomes project, dbSNP version 135 was discarded. Any substitutions observed in more than half of the samples sequenced at> 5% allele frequency were discarded. Small insertions and deletions in the sequence were predicted using GATK. All remaining putative mutations were annotated with sequence ontology terms to indicate the results and position for Ensembl gene annotation. In this final list, all nonsense or missense exon mutations and splicing mutations with an allelic frequency of 10% or more at loci covered at least 100-fold were retained.

  Due to poor sequence coverage in all samples, three genes, TLR1, TLR7 and TLR9 were removed at this stage, leaving a total of 23 genes for further analysis.

To confirm the called mutation, all non-synonymous mutations identified from Fluidigm Access Array sequencing were reamplified using a CS1 tag / CS2 tagged primer pair targeting the region and DNA from the original sample did. If available, DNA from matching normal samples (blood, duodenum or normal squamous epithelium) was also amplified using the same tagged primer pair. Amplification was performed using 5 μl of reaction solution (0.1 Phusion® high fidelity DNA polymerase (New England BioLabs), 1 × Phusion buffer, 4.5 mM MgCl ₂ , 5% DMSO, 0.2 mM dNTP, 1 μM. The forward and reverse primers were run in 25 ng genomic DNA The PCR cycle conditions were as follows: 50 ° C. for 2 minutes, 70 ° C. for 20 minutes, 95 ° C. for 10 minutes, then 95 ° C. 10 cycles of 15 seconds at 60 ° C., 30 seconds at 60 ° C. and 1 minute at 72 ° C., then 15 seconds at 95 ° C., 30 seconds at 80 ° C., 30 seconds at 60 ° C. and 1 cycle at 72 ° C. 2 cycles of minutes, then 15 cycles at 95 ° C., 30 seconds at 60 ° C. and 8 minutes at 1 minute at 72 ° C., then 15 cycles at 95 ° C., 30 seconds at 80 ° C., 60 ° C. 2 cycles of 30 minutes and 1 minute at 72 ° C 8 cycles of 95 ° C for 15 seconds, 60 ° C for 30 seconds and 72 ° C for 1 minute, then 95 ° C for 15 seconds, 80 ° C for 30 seconds, 60 ° C for 30 seconds and 5 cycles of 1 minute at 72 ° C. After amplification, 2 μl of each PCR reaction was collected and pooled into 12 reaction batches so that each pool contained only unique amplicons, then 5 μl pooled. The reaction mix was added to 2 μl of ExoSAP-IT® (Affymetrix) Samples were incubated for 15 minutes at 37 ° C. and then for 15 minutes at 80 ° C. The resulting product was washed in sterile water. Dilute 1: 100 and further 15 cycles of PCR (0.1 unit Phusion® high fidelity DNA polymerase (New England BioLabs), 1 × Phusion buffer, 4.5 mM MgCl ₂ , 5% DMSO, 0 .2 mM Bind Illumina sequencing adapter and 10 bp barcode to each pool using PCR products (1: 100 dilution) treated with dNTPs, 1 μM forward and reverse barcoded primers, 1 μl ExoSAP-IT® The cycle conditions were as follows: thermal activation at 95 ° C. for 2 minutes, then 15 cycles at 95 ° C. for 15 seconds, 60 ° C. for 30 seconds and 72 ° C. for 1 minute. And then a final extension step of 3 minutes at 72 ° C.

  As before, PCR products after barcode addition were first analyzed using an Agilent 2100 BioAnalyzer to ensure that the expected amplicon size was obtained. These were then pooled together and purified using AMPure XP beads using a 1.8: 1.0 bead to amplicon ratio. The library was quantified with a Lightcycler® 480 (Roche) using a KAPA-library quantification kit (KAPA Biosystems), diluted to 2 nM, Illumina clustered and Illumina MiSeq (150 bp paired end). Were subjected to sequencing. The reading was demultiplexed with a known list of barcodes that allowed zero mismatch. Each set of readings is independent of the hg19 reference genome using BWA in paired-end mode (Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60 (2009)) And aligned. Use Samtoolsmpileupvl.17 (Li, H. et al. The Sequence Alignment / Map format and SAMtools. Bioinformatics 25, 2078-9 (2009)) to obtain a count for each nucleotide at the position of the putative somatic mutation. It was. Samples with mutant allele frequency ≧ 3% and coverage depth ≧ 50 were considered confirmed mutations. Furthermore, the mutant allele frequency in matching normals was required to be <1%. We further removed from the samples all mutations with no matching normals, which were confirmed to be germline in a cohort of samples with matched normals that were sequenced.

Capsule sponge specimen processing
Cytosponge ™ capsules were swallowed by the patient and then immediately placed in a preservative solution at 4 ° C. until further processing. The sample was vortexed well and shaken vigorously to remove any cells from the sponge material. The preservative solution containing the cells was centrifuged at 1000 RPM for 5 minutes to pellet the cells. The resulting pellet was resuspended in 500 μL of plasma and thrombin (Diagnostic reagents, Oxford, UK) was then added in 10 μL increments until a clot was formed. The clot was then processed into a paraffin block after being placed in formalin for 24 hours. An 8 × 10 micrometer section was cut and placed in a tube for DNA extraction.

DNA extraction from Cytosponge samples Genomic DNA was removed from 8 × 10 μm sections of treated Cytosponge ™ FFPE clots using deparaffinized buffer (Qiagen) and QIAamp FFPE DNA tissue kit (Qiagen). Extracted. The protocol is the manufacturer except that the sample was incubated at 56 ° C. for 24 hours instead of the 1 hour described, and 10 μl of excess proteinase K was added to the sample after approximately half of the 24 hour incubation. Followed as described by. After extraction, DNA was quantified using the Qubit ™ dsDNA HS assay kit (Invitrogen).

Sequencing for TP53 mutations The coding region of the TP53 gene was sequenced using a multiplexed TP53 PCR assay. Multiplexing consists of 14 primer pairs (Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4, 136ra68 (2012)). Divided into three different pools. The respective sequences of the primers, the genomic region they amplify (coordinates are correct for the hg19 version of the human genome) and which pool they are part of are listed in Tables 12 and 13.

  All p53 multiplexed PCR was performed in duplicate using a Q5 hot start high fidelity 2 × master mix (New England Biolabs). The coding region of the TP53 gene was first amplified using a PCR mix consisting of 1 × Q5 master mix, 5% DMSO, each primer pair at a final concentration of 50 nM and up to 70 ng FFPE DNA extracted from Cytosponge samples. The cycling conditions for PCR were initial denaturation at 95 ° C. for 30 seconds, followed by 30 cycles of 95 ° C. for 10 seconds, 60 ° C. for 10 seconds and 72 ° C. for 15 seconds. Ensuring extension of all PCR products, including a final extension of 2 minutes at 72 ° C.

  After the first round of PCR, 2.5 ul pool 1 and 2.5 ul pool 2 were pooled together. Add 2 microliters of IllustraExostar 1-Step (GE Healthcare UK Ltd) to 5 ul of pooled PCR product and perform Exostar reaction (15 minutes at 37 ° C, then 15 minutes at 80 ° C) 1 Primers from the second reaction were degraded. One microliter of the pooled Exostar treatment product was then added to the barcode PCR to add a unique barcode and a sequencing primer was added to the PCR product. The barcode used for this second PCR was obtained from Forshew et al (Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4, 136ra68 (2012)). Thus, the core sequence of the barcode primer can be found in Table 14. These primers were used because the Fluidigm barcode primer contains the CS1 and CS2 sequences present in the original p53 primer and sequences that bind to the Illumina adapter. The barcode PCR mix consisted of 1 × Q5 master mix, 5% DMSO, each barcode primer pair at a final concentration of 400 nM and 1 ul of undiluted Exostar treated DNA. PCR cycle conditions were initial denaturation at 98 ° C. for 30 seconds, followed by 14 cycles of 98 ° C. for 10 seconds, 60 ° C. for 10 seconds and 72 ° C. for 30 seconds. Ensuring extension of all PCR products, including a final extension of 2 minutes at 72 ° C.

TAm-seq SNV and indel call indel to detect TP53 mutations in Cytosponge ™ samples were called by selecting outliers from locus-specific distributions of background mutation rates. Candidate insertions and deletions in each sample were scored by z-score compared to insertion and deletion rates at the same locus in samples from all other patients. An indel with a z score of 10 or higher, a coverage of at least 200 × and at least 5 support readings was retained.

References on the method of Example 10
1. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60 (2009)
2. Larson, DE et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 28, 311-7 (2012)
3. Koboldt, DC et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.Genome Res 22, 568-76 (2012)
4. Li, H. et al. The Sequence Alignment / Map format and SAMtools. Bioinformatics 25, 2078-9 (2009)
5. Ye, K., Schulz, MH, Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.Bioinformatics 25, 2865-71 (2009)
6. Shah, SP et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers.Nature 486, 395-9 (2012)
7. Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.Sci Transl Med 4, 136ra68 (2012)

Reference for Example 10
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2. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366, 883-92 (2012)
3. Jones, S. et al. Comparative lesion sequencing provides insights into tumor evolution.Proc Natl Acad Sci USA 105, 4283-8 (2008)
4. Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012)
5. Vogelstein, B. et al. Genetic alterations during colorectal-tumor development. N Engl J Med 319, 525-32 (1988)
6. Goh, XY et al. Integrative analysis of array-comparative genomic hybridization and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma. Gut 60, 1317-26 (2011)
7. Quante, M. et al. Bile acid and inflammation activate gastric cardia stem cells in a mouse model of Barrett-like metaplasia.Cancer Cell 21, 36-51 (2012)
8. Greaves, M. & Maley, CC Clonal evolution in cancer.Nature 481, 306-13 (2012)
9. Varghese, S., Lao-Sirieix, P. & Fitzgerald, RC Identification and clinical implementation of biomarkers for Barrett's esophagus. Gastroenterology 142, 435-441 e2 (2012)
10. Dulak, AM et al. Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis. Cancer Res (2012)
11. Dulak, AM et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet 45, 478-86 (2013)
12. Agrawal, N. et al. Comparative genomic analysis of esophageal adenocarcinoma and squamous cell carcinoma. Cancer Discov (2012)
13. Corley, DA et al. Impact of Endoscopic Surveillance on Mortality From Barrett's Esophagus-Associated Esophageal Adenocarcinomas. Gastroenterology 145, 312-319 e1 (2013)
14. Shaheen, NJ & Hur, C. Garlic, Silver Bullets, and Surveillance Upper Endoscopy for Barrett's Esophagus. Gastroenterology 145, 273-6 (2013)
15. Hayes, DF et al. Breaking a vicious cycle. Sci Transl Med 5, 196cm6 (2013)
16. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-93 (2012)
17. Fujimoto, A. et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet 44, 760-4 (2012)
18. Bass, AJ et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet 43, 964-8 (2011)
19. Streppel, MM et al. Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett's esophagus. Oncogene (2013)
20. Curvers, WL et al. Low-grade dysplasia in Barrett's esophagus: overdiagnosed and underestimated. Am J Gastroenterol 105, 1523-30 (2010)
21. Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet 43, 1219-23 (2011)
22. Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228-31 (2010)
23. Reid, BJ, Li, X., Galipeau, PC & Vaughan, TL Barrett's oesophagus and oesophageal adenocarcinoma: time for a new synthesis. Nat Rev Cancer 10, 87-101 (2010)
24. Kadri, SR et al. Acceptability and accuracy of a non-endoscopic screening test for Barrett's oesophagus in primary care: cohort study.BMJ 341, c4372 (2010)
25. Lao-Sirieix, P. et al. Non-endoscopic screening biomarkers for Barrett's oesophagus: from microarray analysis to the clinic.Gut 58, 1451-9 (2009)
26. Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.Sci Transl Med 4, 136ra68 (2012)
27. Dawson, SJ et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 368, 1199-209 (2013)
28. Theisen, J. et al. Preoperative chemotherapy unmasks underlying Barrett's mucosa in patients with adenocarcinoma of the distal esophagus. Surg Endosc 16, 671-3 (2002)
29. Bhat, S. et al. Risk of malignant progression in Barrett's esophagus patients: results from a large population-based study.J Natl Cancer Inst 103, 1049-57 (2011)
30.Nowell, PC The clonal evolution of tumor cell populations. Science 194, 23-8 (1976)
31. Mutter, GL et al. Molecular identification of latent precancers in histologically normal endometrium. Cancer Res 61, 4311-4 (2001)
32. Kinde, I. et al.Evaluation of DNA from the Papanicolaou test to detect ovarian and endometrial cancers.Sci Transl Med 5, 167ra4 (2013)
33. Maley, CC et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet 38, 468-73 (2006)

Statistical Analysis Here we detail a statistical analysis showing the effect of different biomarker combinations on sensitivity and specificity. The data appears to be very good, and it is certainly advantageous to assay four biomarkers. There are two tables below, one for highly dysplasia only and one for any dysplasia.

  Table showing results from any dysplasia (mild, severe and uncertain):

Table showing results from only severe dysplasia:

  The score in the last column is the sum of sensitivity and specificity. It is still important to look at these separately and consider the variance.

  Thus, marker combinations can be selected to maximize sensitivity while minimizing loss of specificity.

In this example, we demonstrate the ability of risk stratified biomarkers to detect dysplasia with Cytosponge ™.
LGD = mild dysplasia HGD / IMC = high grade dysplasia / mucosal carcinoma

  In this example, we present p53 IHC and nucleic acid (by sequencing) data either separately or together.

  Although illustrative embodiments of the present invention have been disclosed in detail herein with reference to the accompanying drawings, the present invention is not limited to these precise embodiments, and the appended claims and their It will be understood that various changes and modifications may be made by those skilled in the art without departing from the scope of the invention as defined by the equivalents.

References
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Claims (30)

A method for assisting in detecting surface abnormalities of a subject's esophagus, wherein the surface abnormalities are mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and intramucosal cancer (IMC). And the method is selected from the group consisting of
a) providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the esophagus of the subject;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3;
Detection of an abnormal level of the at least two markers means that the likelihood of a surface abnormality of the subject's esophagus is increased. Step (b)
(1) cells
(I) p53;
(Ii) c-Myc;
Contacting with a reagent for detecting at least a first molecular marker selected from (iii) AURKA or PLK1, preferably AURKA; and (iv) methylation of MyoD and Runx3;
(2) The method according to claim 1, comprising contacting the cell with a reagent for detecting at least a second molecular marker selected from (i) to (iv).   3. A method according to claim 1 or 2, wherein abnormal levels of at least three of the markers are assayed.   4. The method according to any of claims 1 to 3, wherein abnormal levels of at least four of the markers are assayed.   5. The method of any of claims 1-4, further comprising assaying the cell for atypical properties.   6. A method according to any of claims 1-5, wherein the cells are recovered by unbiased sampling of the surface of the esophagus.   The method of claim 6, wherein the cells are harvested using a capsule sponge.   Before the cell is contacted with a reagent for detecting the molecular marker, (i) pelleting the cell by centrifugation; (ii) resuspending the cell in plasma; (iii) The method according to any one of claims 1 to 7, which is prepared by adding thrombin and incubating until a clot is formed.   9. The method of claim 8, further comprising the steps of incubating the clot in formalin, processing to paraffin blocks, and slicing into sections suitable for microscopy.   The method according to any of claims 1 to 9, wherein p53 is evaluated by immunohistochemistry.   10. The method according to any of claims 1 to 9, wherein p53 is evaluated by detection of one or more p53 mutations.   10. The method according to any of claims 1 to 9, wherein p53 is assessed by immunohistochemistry and p53 is also assessed by detection of one or more p53 mutations.   The method according to claim 1, wherein cMyc is evaluated by immunohistochemistry.   14. A method according to any of claims 1 to 13, wherein AURKA is assessed by immunohistochemistry.   15. The method of any of claims 1-14, wherein methylation of MyoD / Runx3 is assessed by MethyLight analysis.   7. The method of claim 6, wherein atypicality is assessed by scoring cells for their morphology according to the Wien scale.   17. A method according to any of claims 1-16, wherein the step of assaying the cells for TFF3 precedes step (b) of the method. An assay for selecting a treatment regimen comprising:
a) providing a sample of cells from a subject, the sample comprising cells recovered from the surface of the subject's esophagus;
b) said cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3;
The assay wherein an endoscopy and biopsy treatment regimen is selected when two abnormal levels of the at least two markers are detected. (A) an apparatus or system configured to analyze an esophageal sample from a subject, said analysis comprising:
(B) cells
(I) p53;
(Ii) c-Myc;
Assaying for at least two markers selected from (iii) AURKA; and (iv) methylation of MyoD and Runx3;
The apparatus or system includes an output module;
If at least two abnormal levels of the marker are detected, the output module indicates an increased likelihood of a surface abnormality in the esophagus for the subject, the surface abnormality is mild dysplasia (LGD) ), High dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and intramucosal cancer (IMC).   Use of a substance that recognizes, binds to, or has affinity for a methylation of a polypeptide or a nucleic acid sequence for use in assisting detection of a surface abnormality of an esophagus of the subject Is selected from the group consisting of mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and intramucosal cancer (IMC), wherein the polypeptide and / or nucleic acid sequence is The use as defined in any one of Items 1 to 16.   21. Use according to claim 20, wherein each of the substances recognizes, binds to or has an affinity for one or more of the polypeptide or nucleic acid sequences, respectively.   An assay device for use in assisting detection of a surface abnormality of a subject's esophagus, said surface abnormality comprising mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and A solid selected from the group consisting of intramucosal carcinoma (IMC), wherein the assay device recognizes, binds to or binds to or has affinity for a polypeptide or a nucleic acid sequence methylation 17. The assay device comprising a substrate, wherein the polypeptide and / or nucleic acid sequence is as defined in any of claims 1-16. (I) p53 in a biological sample;
(Ii) c-Myc;
(Iii) AURKA
And a reagent for determining the methylation level of MyoD and Runx3. A method for assisting in detecting surface abnormalities of a subject's esophagus
The surface abnormality is selected from the group consisting of mild dysplasia (LGD), severe dysplasia (HGD), asymptomatic esophageal adenocarcinoma (OAC) and intramucosal cancer (IMC);
Said method comprising providing a sample of cells from said subject, said sample comprising cells recovered from the surface of said subject's esophagus; and assaying said cells for TFF3. Including
When TFF3 is detected in the cells of the sample, the method according to any one of claims 1 to 16 is performed, and in addition to detecting TFF3, detection of an abnormal level of at least one marker is performed on the subject. The method wherein the likelihood of a surface abnormality of the esophagus is increasing.   At least two markers in addition to detection of TFF3, preferably at least three markers in addition to detection of TFF3, preferably at least four markers in addition to detection of TFF3, preferably all five markers in addition to detection of TFF3 25. The method of claim 24, wherein detection of indicates that the likelihood of a surface abnormality in the subject's esophagus is increasing.   26. A method according to claim 24 or 25, wherein the cells are recovered by unbiased sampling of the surface of the esophagus.   27. The method of claim 26, wherein the cells are harvested using a capsule sponge. A method for assisting in detecting surface abnormalities in a subject's esophagus,
The surface abnormality is esophageal adenocarcinoma (OAC);
The method includes providing a sample of cells from the subject, the sample comprising cells recovered from the surface of the subject's esophagus, and assaying the cells for SMAD4. ,
The method wherein the detection of SMAD4 in the cells of the sample indicates an increased likelihood of esophageal adenocarcinoma (OAC) of the esophagus of the subject.   A method substantially as herein described. A method substantially as herein described with reference to the drawings.